Cryo-EM structure of the human SSU processome, state pre-A1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7mq8
Q-score: 0.417
Singh S, Vanden Broeck A, Miller L, Chaker-Margot M, Klinge S
Science (2021) 373 pp. eabj5338-eabj5338 [ Pubmed: 34516797 DOI: doi:10.1126/science.abj5338 ]
- Human ssu processome (5 MDa, Complex from Homo sapiens)
- Bystin (33 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 4 homolog (76 kDa, Protein from Homo sapiens)
- Rrna 2'-o-methyltransferase fibrillarin (33 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (12 kDa, Protein from Homo sapiens)
- Nucleolar protein 7 (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Homo sapiens)
- Nucleolar complex protein 4 homolog (50 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 18 homolog (62 kDa, Protein from Homo sapiens)
- Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
- Rrna-processing protein fcf1 homolog (23 kDa, Protein from Homo sapiens)
- Protein aatf (63 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- U3 small nucleolar ribonucleoprotein protein mpp10 (78 kDa, Protein from Homo sapiens)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 15 homolog (58 kDa, Protein from Homo sapiens)
- Something about silencing protein 10 (54 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Neuroguidin (35 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 43 (74 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Heat repeat-containing protein 1 (242 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 5'ets rrna (1 MDa, RNA from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Unassigned peptides (23 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 18s rrna (602 kDa, RNA from Homo sapiens)
- 5'ets rrna (4 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 36 (105 kDa, Protein from Homo sapiens)
- Ribosome biogenesis protein bms1 homolog (145 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 6 homolog (70 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 14 homolog a (88 kDa, Protein from Homo sapiens)
- Probable u3 small nucleolar rna-associated protein 11 (30 kDa, Protein from Homo sapiens)
- Rna-binding protein pno1 (27 kDa, Protein from Homo sapiens)
- Uncharacterized protein c1orf131 (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 46 (68 kDa, Protein from Homo sapiens)
- Rna cytidine acetyltransferase (115 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Unassigned peptide (3 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Ribosomal rna small subunit methyltransferase nep1 (26 kDa, Protein from Homo sapiens)
- Nucleolar protein 6 (127 kDa, Protein from Homo sapiens)
- Rrp12-like protein (73 kDa, Protein from Homo sapiens)
- Periodic tryptophan protein 2 homolog (102 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Deoxynucleotidyltransferase terminal-interacting protein 2 (84 kDa, Protein from Homo sapiens)
- Nucleolar protein 10 (80 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 3 (106 kDa, Protein from Homo sapiens)
- Ribosomal rna-processing protein 7 homolog a (32 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Krr1 small subunit processome component homolog (43 kDa, Protein from Homo sapiens)
- Nucleolar protein 11 (73 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 75 (94 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 13 (51 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-interacting protein 2 (51 kDa, Protein from Homo sapiens)
- U3 snorna (70 kDa, RNA from Homo sapiens)
- Nucleolar protein 14 (68 kDa, Protein from Homo sapiens)
- Nucleolar protein 56 (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Small subunit processome component 20 homolog (318 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Nucleolar protein 58 (59 kDa, Protein from Homo sapiens)
- Transducin beta-like protein 3 (89 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human SSU processome, state pre-A1*
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 7mq9
Q-score: 0.357
Singh S, Vanden Broeck A, Miller L, Chaker-Margot M, Klinge S
Science (2021) 373 pp. eabj5338-eabj5338 [ Pubmed: 34516797 DOI: doi:10.1126/science.abj5338 ]
- Ribosome biogenesis protein bms1 homolog (146 kDa, Protein from Homo sapiens)
- Deoxynucleotidyltransferase terminal-interacting protein 2 (84 kDa, Protein from Homo sapiens)
- Human ssu processome (5 MDa, Complex from Homo sapiens)
- Nucleolar protein 10 (80 kDa, Protein from Homo sapiens)
- Bystin (33 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 3 (106 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Uncharacterized protein c1orf131 (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 15 homolog (58 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 46 (68 kDa, Protein from Homo sapiens)
- Ribosomal rna-processing protein 7 homolog a (32 kDa, Protein from Homo sapiens)
- Something about silencing protein 10 (54 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 4 homolog (76 kDa, Protein from Homo sapiens)
- Rna cytidine acetyltransferase (115 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Rrna 2'-o-methyltransferase fibrillarin (33 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 43 (74 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (12 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Krr1 small subunit processome component homolog (43 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Heat repeat-containing protein 1 (242 kDa, Protein from Homo sapiens)
- Unassigned peptides (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Probable u3 small nucleolar rna-associated protein 11 (30 kDa, Protein from Homo sapiens)
- 5'ets rrna (1 MDa, RNA from Homo sapiens)
- Nucleolar protein 7 (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4 x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Rna-binding protein pno1 (27 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 36 (105 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 75 (94 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 13 (51 kDa, Protein from Homo sapiens)
- Nucleolar complex protein 4 homolog (50 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 18 homolog (62 kDa, Protein from Homo sapiens)
- Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
- Rrna-processing protein fcf1 homolog (23 kDa, Protein from Homo sapiens)
- 5' ets rrna (7 kDa, RNA from Homo sapiens)
- U3 small nucleolar rna-interacting protein 2 (51 kDa, Protein from Homo sapiens)
- Nucleolar protein 11 (75 kDa, Protein from Homo sapiens)
- Protein aatf (63 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- U3 snorna (70 kDa, RNA from Homo sapiens)
- Nucleolar protein 14 (68 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- U3 small nucleolar ribonucleoprotein protein mpp10 (78 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 6 homolog (70 kDa, Protein from Homo sapiens)
- Nucleolar protein 56 (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Homo sapiens)
- Ribosomal rna small subunit methyltransferase nep1 (26 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 14 homolog a (88 kDa, Protein from Homo sapiens)
- Nucleolar protein 6 (127 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Rrp12-like protein (73 kDa, Protein from Homo sapiens)
- Small subunit processome component 20 homolog (318 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Nucleolar protein 58 (59 kDa, Protein from Homo sapiens)
- Periodic tryptophan protein 2 homolog (102 kDa, Protein from Homo sapiens)
- Transducin beta-like protein 3 (89 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human SSU processome, state post-A1
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7mqa
Q-score: 0.526
Singh S, Vanden Broeck A, Miller L, Chaker-Margot M, Klinge S
Science (2021) 373 pp. eabj5338-eabj5338 [ Pubmed: 34516797 DOI: doi:10.1126/science.abj5338 ]
- Ribosome biogenesis protein bms1 homolog (146 kDa, Protein from Homo sapiens)
- Deoxynucleotidyltransferase terminal-interacting protein 2 (84 kDa, Protein from Homo sapiens)
- Human ssu processome (5 MDa, Complex from Homo sapiens)
- Bystin (33 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 3 (106 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 15 homolog (58 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 46 (68 kDa, Protein from Homo sapiens)
- Ribosomal rna-processing protein 7 homolog a (32 kDa, Protein from Homo sapiens)
- Something about silencing protein 10 (54 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 4 homolog (76 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Rrna 2'-o-methyltransferase fibrillarin (33 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 43 (74 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (12 kDa, Protein from Homo sapiens)
- Unassigned peptides (19 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Probable atp-dependent rna helicase dhx37 (129 kDa, Protein from Homo sapiens)
- Heat repeat-containing protein 1 (242 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Nucleolar protein 11 (73 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Probable u3 small nucleolar rna-associated protein 11 (30 kDa, Protein from Homo sapiens)
- 5'ets rrna (1 MDa, RNA from Homo sapiens)
- Nucleolar protein 7 (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Rna-binding protein pno1 (27 kDa, Protein from Homo sapiens)
- 18s rrna (604 kDa, RNA from Homo sapiens)
- Wd repeat-containing protein 36 (105 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 75 (94 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 13 (51 kDa, Protein from Homo sapiens)
- Nucleolar complex protein 4 homolog (50 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 18 homolog (62 kDa, Protein from Homo sapiens)
- Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-interacting protein 2 (51 kDa, Protein from Homo sapiens)
- Rrna-processing protein fcf1 homolog (23 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- U3 snorna (70 kDa, RNA from Homo sapiens)
- Nucleolar protein 14 (68 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Exosome component 10 (100 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- U3 small nucleolar ribonucleoprotein protein mpp10 (78 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 6 homolog (70 kDa, Protein from Homo sapiens)
- Probable dimethyladenosine transferase (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Nucleolar protein 56 (66 kDa, Protein from Homo sapiens)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Homo sapiens)
- Ribosomal rna small subunit methyltransferase nep1 (26 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 14 homolog a (88 kDa, Protein from Homo sapiens)
- Nucleolar protein 6 (127 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Rrp12-like protein (73 kDa, Protein from Homo sapiens)
- Small subunit processome component 20 homolog (318 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Active regulator of sirt1 (15 kDa, Protein from Homo sapiens)
- Nucleolar protein 58 (59 kDa, Protein from Homo sapiens)
- Periodic tryptophan protein 2 homolog (102 kDa, Protein from Homo sapiens)
- Transducin beta-like protein 3 (89 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 7ado
Q-score: 0.458
Miller-Vedam LE, Brauning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS
eLife (2020) 9 [ DOI: doi:10.7554/eLife.62611 Pubmed: 33236988 ]
- Er membrane protein complex subunit 10 (27 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 2 (34 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Er membrane protein complex subunit 1 (111 kDa, Protein from Homo sapiens)
- Unassigned helix (1 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 4 (20 kDa, Protein from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Human endoplasmic reticulum membrane protein complex (emc) in popc nanodiscs (300 kDa, Complex from Homo sapiens)
- Er membrane protein complex subunit 3 (29 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 8 (23 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 7 (26 kDa, Protein from Homo sapiens)
- Membrane magnesium transporter 1 (15 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 6 (12 kDa, Protein from Homo sapiens)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7kra
Q-score: 0.474
Miller-Vedam LE, Brauning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS
eLife (2020) 9 [ DOI: doi:10.7554/eLife.62611 Pubmed: 33236988 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Er membrane protein complex subunit 1 (87 kDa, Protein from Saccharomyces cerevisiae)
- Endoplasmic reticulum membrane protein complex subunit 10 (22 kDa, Protein from Saccharomyces cerevisiae)
- Er membrane protein complex subunit 2 (33 kDa, Protein from Saccharomyces cerevisiae)
- Fab dh4 heavy chain (26 kDa, Protein from Homo sapiens)
- Fab dh4 light chain (25 kDa, Protein from Homo sapiens)
- Er membrane protein complex subunit 4 (21 kDa, Protein from Saccharomyces cerevisiae)
- Unassigned helix (2 kDa, Protein from Saccharomyces cerevisiae)
- Fab dh4 (Complex from Homo sapiens)
- Er membrane protein complex subunit 3 (28 kDa, Protein from Saccharomyces cerevisiae)
- Protein sop4 (26 kDa, Protein from Saccharomyces cerevisiae)
- [(2~{r})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate (524 Da, Ligand)
- Er membrane protein complex subunit 5 (20 kDa, Protein from Saccharomyces cerevisiae)
- Endoplasmic reticulum membrane protein complex (Complex from Saccharomyces cerevisiae)
- S. cerevisiae endoplasmic reticulum membrane protein complex (emc) bound to fab dh4 in yeast total extract lipid nanodiscs (Complex)
- Er membrane protein complex subunit 6 (12 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7ktx
Q-score: 0.287
Miller-Vedam LE, Brauning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS
eLife (2020) 9 [ DOI: doi:10.7554/eLife.62611 Pubmed: 33236988 ]
- Unassigned helix (2 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 5 (20 kDa, Protein from Saccharomyces cerevisiae BY4743)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab dh4 light chain (25 kDa, Protein from Homo sapiens)
- Fab dh4 heavy chain (26 kDa, Protein from Homo sapiens)
- Protein sop4 (26 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Endoplasmic reticulum membrane protein complex (Complex from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 3 (28 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 2 (33 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Fab dh4 (Complex from Homo sapiens)
- Endoplasmic reticulum membrane protein complex subunit 10 (22 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 4 (21 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 1 (87 kDa, Protein from Saccharomyces cerevisiae BY4743)
- Er membrane protein complex subunit 6 (12 kDa, Protein from Saccharomyces cerevisiae BY4743)
- S. cerevisiae endoplasmic reticulum membrane protein complex (emc) bound to fab in ddm detergent (Complex)
cryo-EM structure of transcription coactivator SAGA
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6t9i
Q-score: 0.38
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ DOI: doi:10.1038/s41586-020-1933-5 Pubmed: 31969703 ]
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga complex (1 MDa, Complex from Saccharomyces cerevisiae S288C)
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6t9k
Q-score: 0.473
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P
Nature (2020) 577 pp. 717-720 [ DOI: doi:10.1038/s41586-020-1933-5 Pubmed: 31969703 ]
- Transcription initiation factor tfiid subunit 12 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga core module (500 kDa, Complex from Saccharomyces cerevisiae S288C)
- Unassigned sequence (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription initiation factor tfiid subunit 6 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional activator spt7 (152 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional coactivator hfi1/ada1 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor spt20 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 5 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saga-associated factor 73 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein spt3 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6gaw
Q-score: 0.449
Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N
Nature (2018) 560 pp. 263-267 [ Pubmed: 30089917 DOI: doi:10.1038/s41586-018-0373-y ]
- 39s ribosomal protein l15, mitochondrial (33 kDa, Protein from Sus scrofa)
- Ul23m (17 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s18c (16 kDa, Protein from Sus scrofa)
- Mt-co3 mrna, mitochondrial (63 kDa, RNA from Homo sapiens)
- Mitochondrial ribosomal protein l48 (23 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l27 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l10 (29 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l40, mitochondrial isoform 1 (24 kDa, Protein from Sus scrofa)
- Ml65 (49 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l38 (44 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s25 (19 kDa, Protein from Sus scrofa)
- Ul30m (18 kDa, Protein from Sus scrofa)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- Ms33 (12 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l55, mitochondrial (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s5 (48 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s12 (15 kDa, Protein from Sus scrofa)
- Trna-phe, mitochondrial (23 kDa, RNA from Sus scrofa)
- Mitochondrial ribosomal protein l20 (17 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l2, mitochondrial (33 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Ml54 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s2 (31 kDa, Protein from Sus scrofa)
- Bl32m (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l9 (30 kDa, Protein from Sus scrofa)
- Guanosine-5'-monophosphate (363 Da, Ligand)
- Mitochondrial ribosomal protein l34 (10 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s14 (15 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l52, mitochondrial (13 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Sus scrofa)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Sus scrofa)
- Ul14m (15 kDa, Protein from Sus scrofa)
- Bs16m (15 kDa, Protein from Sus scrofa)
- Spermine (202 Da, Ligand)
- Uncharacterized protein (27 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l46 (32 kDa, Protein from Sus scrofa)
- 5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
- Ml45 (35 kDa, Protein from Sus scrofa)
- N-formylmethionine (177 Da, Ligand)
- Mitochondrial ribosomal protein s6 (14 kDa, Protein from Sus scrofa)
- Ml42 (16 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s18a (22 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l35 (21 kDa, Protein from Sus scrofa)
- Unassigned secondary structure elements (5 kDa, Protein from Sus scrofa)
- Bl33m (7 kDa, Protein from Sus scrofa)
- Bs21m (10 kDa, Protein from Sus scrofa)
- Peptidyl-trna hydrolase ict1, mitochondrial (23 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s24 (18 kDa, Protein from Sus scrofa)
- Ml64 (25 kDa, Protein from Sus scrofa)
- Translation initiation factor if-2, mitochondrial (72 kDa, Protein from Homo sapiens)
- Death associated protein 3 (45 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l37 (47 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l11 (20 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l24, mitochondrial (24 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l57 (12 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l39 (38 kDa, Protein from Sus scrofa)
- Ml53 (12 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l13, mitochondrial (20 kDa, Protein from Sus scrofa)
- P-site fmet-trnamet, mitochondrial (22 kDa, RNA from Homo sapiens)
- Ml50 (18 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l51 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l18 (20 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l21 (23 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- 12s ribosomal rna, mitochondrial (308 kDa, RNA from Sus scrofa)
- Mitochondrial ribosomal protein l19 (33 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l44, mitochondrial (37 kDa, Protein from Sus scrofa)
- Ul22m (24 kDa, Protein from Sus scrofa)
- Sodium ion (22 Da, Ligand)
- Ict1 (38 kDa, Protein from Sus scrofa)
- Ml43 (17 kDa, Protein from Sus scrofa)
- Ribosomal protein (10 kDa, Protein from Sus scrofa)
- Ms27 (51 kDa, Protein from Sus scrofa)
- Us17m (14 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s7 (28 kDa, Protein from Sus scrofa)
- Aurora kinase a interacting protein 1 (22 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l16, mitochondrial (28 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Mitochondrial ribosomal protein l41 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s10 (23 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s26 (23 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s35, mitochondrial (37 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s22 (43 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Sus scrofa)
- Ms31 (44 kDa, Protein from Sus scrofa)
- 16s ribosomal rna, mitochondrial (504 kDa, RNA from Sus scrofa)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Sus scrofa)
- Unassigned secondary structure elements (1 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l47 (30 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l12 (21 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l17, mitochondrial (19 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l28 (30 kDa, Protein from Sus scrofa)
- 28s ribosomal protein s28, mitochondrial (21 kDa, Protein from Sus scrofa)
- Mammalian mitochondrial translation initiation complex (2 MDa, Complex from sus sucorfa)
- Mitochondrial ribosomal protein l4 (33 kDa, Protein from Sus scrofa)
- 39s ribosomal protein l49, mitochondrial (18 kDa, Protein from Sus scrofa)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6gaz
Q-score: 0.462
Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N
Nature (2018) 560 pp. 263-267 [ Pubmed: 30089917 DOI: doi:10.1038/s41586-018-0373-y ]
- Death associated protein 3 (45 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s14 (15 kDa, Protein from Sus scrofa)
- Nucleic acids (Complex from Homo sapiens)
- Mitochondrial ribosomal protein s37 (13 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s9 (45 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s18c (16 kDa, Protein from Sus scrofa)
- Mt-co3 mrna, mitochondrial (63 kDa, RNA from Homo sapiens)
- Translation initiation factor if-2, mitochondrial (72 kDa, Protein from Homo sapiens)
- Mitochondrial ribosomal protein s7 (28 kDa, Protein from Sus scrofa)
- Ms31, mrps31 (44 kDa, Protein from Sus scrofa)
- Aurora kinase a interacting protein 1 (22 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Mitochondrial ribosomal protein s33 (12 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s21 (10 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s10 (23 kDa, Protein from Sus scrofa)
- Spermine (202 Da, Ligand)
- P-site fmet-trnamet, mitochondrial (22 kDa, RNA from Homo sapiens)
- Mitochondrial ribosomal protein s25 (19 kDa, Protein from Sus scrofa)
- Translation initiation factor if-2, mitochondrial (Complex from Homo sapiens)
- Mitochondrial ribosomal protein s26 (23 kDa, Protein from Sus scrofa)
- 5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
- Mitochondrial ribosomal protein s22 (43 kDa, Protein from Sus scrofa)
- Water (18 Da, Ligand)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Sus scrofa)
- Unassigned secondary structure elements (1 kDa, Protein from Sus scrofa)
- N-formylmethionine (177 Da, Ligand)
- Mitochondrial ribosomal protein s5 (48 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s39 (76 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s12 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s6 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Mitochondrial ribosomal protein s35 (37 kDa, Protein from Sus scrofa)
- 12s ribosomal rna, mitochondrial (308 kDa, RNA from Sus scrofa)
- Mitochondrial ribosomal protein l19 (33 kDa, Protein from Sus scrofa)
- Mitoribosomal protein ms28, mrps28 (21 kDa, Protein from Sus scrofa)
- Mammalian mitochondrial translation initiation complex (2 MDa, Complex)
- Zinc ion (65 Da, Ligand)
- Mitochondrial ribosomal protein s34 (25 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s11 (20 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s24 (18 kDa, Protein from Sus scrofa)
- Porcine ribosome (Complex from Sus scrofa)
- Mitochondrial ribosomal protein s15 (27 kDa, Protein from Sus scrofa)
- Sodium ion (22 Da, Ligand)
- Mitochondrial ribosomal protein s2 (31 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s27 (45 kDa, Protein from Sus scrofa)
- Bs16m, mrps16 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s23 (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s17 (14 kDa, Protein from Sus scrofa)