RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8bvw
Q-score: 0.234
Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P
Mol Cell (2023) 83 pp. 1798- [ DOI: doi:10.1016/j.molcel.2023.04.011 Pubmed: 37148879 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (67 kDa, DNA from unidentified adenovirus)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Nucleosome (dna) (Complex from unidentified adenovirus)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Tata-box binding protein (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- General transcription factor iih (490 kDa, Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- General transcription factor iif (Complex from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Mammalian rna polymerase ii (516 kDa, Complex from Sus scrofa)
- General transcription factor iia (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Nucleosome (protein) (Complex from Xenopus laevis)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with the distal +1 nucleosome (1 MDa, Complex)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (88 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iie (Complex from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- General transcription factor iib (Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Non-template dna (67 kDa, DNA from unidentified adenovirus)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Human Mediator with RNA Polymerase II Pre-initiation complex
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7nvr
Q-score: 0.171
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Unassigned peptides (med29 or med30) (Complex from Trichoplusia ni)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Unassigned peptide (med17) (954 Da, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Unassigned peptide (med14) (1 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Unassigned peptide (med6) (1 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Nt (32 kDa, DNA from Human mastadenovirus C)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- Nt and template (Complex from Human mastadenovirus C)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factors (Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Trichoplusia ni)
- Magnesium ion (24 Da, Ligand)
- Pol complex and mediator of rna polymerase ii transcription (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Template (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Unassigned peptide (med29 or med30) (1 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Human mediator with rna polymerase ii pre-initiation complex (Complex)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Resolution: 7.3 Å
EM Method: Single-particle
Fitted PDBs: 7nvy
Q-score: 0.118
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with closed promoter dna in proximal position (1 MDa, Complex)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7nvz
Q-score: 0.111
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Rna polymerase ii pre-initiation complex with closed promoter dna in distal position (1 MDa, Complex)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
RNA polymerase II pre-initiation complex with open promoter DNA
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7nw0
Q-score: 0.119
Aibara S, Schilbach S, Cramer P
Nature (2021) 594 pp. 124-128 [ Pubmed: 33902107 DOI: doi:10.1038/s41586-021-03554-8 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Template dna (32 kDa, DNA from Human mastadenovirus C)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Tfiih basal transcription factor complex helicase xpd subunit (87 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely xpb (698 Da, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (32 kDa, DNA from Human mastadenovirus C)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Rna polymerase ii pre-initiation complex with open promoter dna (1 MDa, Complex)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Unassigned peptide, likely tfiie-beta (1 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
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)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6gb2
Q-score: 0.481
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 ]
- Mitochondrial ribosomal protein l34 (10 kDa, Protein from Sus scrofa)
- Ict1 (38 kDa, Protein from Sus scrofa)
- Mammalian mitochondrial ribosome (Complex from Sus scrofa)
- Mitochondrial ribosomal protein l32 (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l23 (17 kDa, Protein from Sus scrofa)
- 'mitochondrial ribosomal protein l30 (18 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)
- Mitochondrial ribosomal protein l40 (24 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l45 (35 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l15 (33 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l57 (12 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l16 (28 kDa, Protein from Sus scrofa)
- Ml53, mrpl53 (12 kDa, Protein from Sus scrofa)
- Ribosomal protein (10 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l39 (38 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l48 (23 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l42 (16 kDa, Protein from Sus scrofa)
- Translation initiation factor if-2, mitochondrial (72 kDa, Protein from Homo sapiens)
- Mrpl34 (18 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l27 (15 kDa, Protein from Sus scrofa)
- Trna (Complex from Homo sapiens)
- Mitochondrial ribosomal protein l10 (29 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l41 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l44 (37 kDa, Protein from Sus scrofa)
- Spermine (202 Da, Ligand)
- P-site fmet-trnamet, mitochondrial (22 kDa, RNA from Homo sapiens)
- Mitochondrial ribosomal protein l38 (44 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l46 (32 kDa, Protein from Sus scrofa)
- Translation initiation factor if-2, mitochondrial (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Mitochondrial ribosomal protein l43 (17 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l51 (15 kDa, Protein from Sus scrofa)
- 5'-guanosine-diphosphate-monothiophosphate (539 Da, Ligand)
- Mitochondrial ribosomal protein l18 (20 kDa, Protein from Sus scrofa)
- 16s ribosomal rna, mitochondrial (504 kDa, RNA from Sus scrofa)
- Mitochondrial ribosomal protein l13 (20 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l14 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l47 (30 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l33 (7 kDa, Protein from Sus scrofa)
- 'mitochondrial ribosomal protein l59 (25 kDa, Protein from Sus scrofa)
- N-formylmethionine (177 Da, Ligand)
- Mitochondrial ribosomal protein l12 (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l21 (23 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- 'mitochondrial ribosomal protein l55 (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l19 (33 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l20 (17 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein s18a (22 kDa, Protein from Sus scrofa)
- Mammalian mitochondrial translation initiation complex (2 MDa, Complex)
- Mitochondrial ribosomal protein l35 (21 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l28 (30 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l2 (33 kDa, Protein from Sus scrofa)
- Unassigned secondary structure elements (5 kDa, Protein from Sus scrofa)
- Cp trnaphe, mitochondrial (23 kDa, RNA from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Ml65, mrps30 (49 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l58 (23 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l50 (18 kDa, Protein from Sus scrofa)
- Sodium ion (22 Da, Ligand)
- Uncharacterized protein (15 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l22 (24 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l52 (13 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l4 (33 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l9 (30 kDa, Protein from Sus scrofa)
- Mitochondrial ribosomal protein l24 (24 kDa, Protein from Sus scrofa)
- Guanosine-5'-monophosphate (363 Da, Ligand)
- Mitochondrial ribosomal protein l17 (19 kDa, Protein from Sus scrofa)