Structure of the human 48S initiation complex in open state (h48S AUG open)
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7qp6
Q-score: 0.233
Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N
Nucleic Acids Res (2022) 50 pp. 5282-5298 [ DOI: doi:10.1093/nar/gkac283 Pubmed: 35489072 ]
- Human 48s initiation complex 40s-eif1-eif1a-eif2-eif3-trna-met-mrna (Complex)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Mrna (6 kDa, RNA from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
Structure of the human 48S initiation complex in closed state (h48S AUG closed)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7qp7
Q-score: 0.337
Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N
Nucleic Acids Res (2022) 50 pp. 5282-5298 [ Pubmed: 35489072 DOI: doi:10.1093/nar/gkac283 ]
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Human 48s initiation complex 40s-eif1-eif1a-eif2-eif3-trna-met-mrna (Complex)
Structural basis of Integrator-mediated transcription regulation
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pks
Q-score: 0.278
Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P
Science (2021) 374 pp. 883-887 [ DOI: doi:10.1126/science.abk0154 Pubmed: 34762484 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Template dna (Complex from Human immunodeficiency virus 1)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Rpbi c-terminal domain peptide (1 kDa, Protein from Sus scrofa domesticus)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dsif (Complex from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Nelf (Complex from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ted
Q-score: 0.338
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P
Nat Struct Mol Biol (2020) 27 pp. 668-677 [ DOI: doi:10.1038/s41594-020-0437-1 Pubmed: 32541898 ]
- Dna/rna (Complex from synthetic construct)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna (37-mer) (14 kDa, DNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Complete ec* (1 MDa, Complex)
- Uncharacterized protein (7 kDa, Protein from Sus scrofa)
- Pig dna/rna polymerase subunits (Complex from Sus scrofa)
- Transcription elongation factor spt4 and spt5 (Complex from Homo sapiens)
- Human transcription factors and associated proteins (Complex from Homo sapiens)
- Uncharacterized protein (13 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit c (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*ap*ap*cp*cp*gp*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (14 kDa, RNA from synthetic construct)
Structure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map A)
Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P
Nature (2018) 560 pp. 607-612 [ DOI: doi:10.1038/s41586-018-0440-4 Pubmed: 30135578 ]
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Nucleic acids (Complex from synthetic construct)
- Associated proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Ctr9,rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein ctr9 homolog (125 kDa, Protein from Homo sapiens)
- Leo1,leo1,rna polymerase-associated protein leo1 (84 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit g (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Transcription elongation factor spt6,transcription elongation factor spt6,transcription elongation factor spt6 (198 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit c (31 kDa, Protein from Sus scrofa)
- Rna (14 kDa, RNA from synthetic construct)
- Rpb11 (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Template dna (14 kDa, DNA from synthetic construct)
- Rna polymerase ii (Complex from Sus scrofa)
- Paf1,rna polymerase ii-associated factor 1 homolog,rna polymerase ii-associated factor 1 homolog (67 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii-dsif-paf-spt6 elongation complex (ec*) (1 MDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Cdc73 (1 kDa, Protein from Homo sapiens)