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human RNA polymerase III pre-initiation complex closed DNA 1
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8ity
Q-score: 0.291
Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y
Cell Res (2023) 33 pp. 565-568 [ DOI: doi:10.1038/s41422-023-00819-x Pubmed: 37165065 ]
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex closed complex 1 (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Dna (82-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (35 kDa, Protein from Homo sapiens)
- Dna (82-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex closed complex 1 (Complex)
- Transcription factor tfiiib component b'' homolog (294 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7uwh
Q-score: 0.458
Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E
Cell (2023) 186 pp. 2425- [ DOI: doi:10.1016/j.cell.2023.04.029 Pubmed: 37196657 ]
- Dna/rna (59-mer) (18 kDa, Macromolecule from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Ribonuclease hii (21 kDa, Protein from Escherichia coli)
- Dna (59-mer) (18 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Rna (18-mer) (5 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Elongation complex(ec)-rnaseh2 complex bound to ribonucleotide substrate (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
RNA polymerase III pre-initiation complex melting complex 1
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8iue
Q-score: 0.291
Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y
Cell Res (2023) 33 pp. 565-568 [ DOI: doi:10.1038/s41422-023-00819-x Pubmed: 37165065 ]
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Transcription factor (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Human gene for u 6 rna (143 kDa, DNA from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna (74-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex melting complex 1 (1 MDa, Complex from Homo sapiens)
- Transcription factor tfiiib component b'' homolog (294 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase (Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
RNA polymerase III pre-initiation complex open complex 1
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8iuh
Q-score: 0.341
Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y
Cell Res (2023) 33 pp. 565-568 [ DOI: doi:10.1038/s41422-023-00819-x Pubmed: 37165065 ]
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex closed complex 1 (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii, snapc (Complex)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Tfiiib (Complex)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna (81-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Dna (81-mer) (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Transcription factor tfiiib component b'' homolog (294 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
Human DNA polymerase alpha/primase elongation complex I bound to primer/template
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8d96
Q-score: 0.426
He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH
Nat Struct Mol Biol (2023) 30 pp. 579-583 [ Pubmed: 37069376 DOI: doi:10.1038/s41594-023-00971-3 ]
- Dna/rna (5'-gtp)-r(p*gp*cp*gp*gp*cp*ap*cp*g)-d(p*ap*cp*c)-3') (3 kDa, Macromolecule from Homo sapiens)
- Dna primase large subunit (58 kDa, Protein from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
- Dna (5'-d(*ap*tp*ap*ap*tp*gp*gp*tp*cp*gp*tp*gp*cp*cp*gp*cp*cp*ap*ap*tp*ap*a)-3') (6 kDa, DNA from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna polymerase alpha catalytic subunit (166 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Elongation complex i of human dna polymerase alpha/primase bound to rna-dna primer and dna template (340 kDa, Complex from Homo sapiens)
Human DNA polymerase-alpha/primase elongation complex II bound to primer/template
Resolution: 3.59 Å
EM Method: Single-particle
Fitted PDBs: 8d9d
Q-score: 0.347
He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH
Nat Struct Mol Biol (2023) 30 pp. 579-583 [ Pubmed: 37069376 DOI: doi:10.1038/s41594-023-00971-3 ]
- Elongation complex ii of human dna polymerase alpha/primase bound to rna-dna primer and dna template (340 kDa, Complex from Homo sapiens)
- Dna (5'-d(*ap*tp*gp*gp*tp*cp*gp*tp*gp*cp*cp*gp*cp*cp*ap*ap*tp*ap*a)-3') (5 kDa, DNA from Homo sapiens)
- Dna primase large subunit (58 kDa, Protein from Homo sapiens)
- Dna/rna (5'-d(*(gtp))-r(p*gp*cp*gp*gp*cp*ap*cp*g)-d(p*ap*cp*c)-3') (3 kDa, Macromolecule from Homo sapiens)
- 2'-deoxyadenosine 5'-triphosphate (491 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna primase small subunit (49 kDa, Protein from Homo sapiens)
- Dna polymerase alpha catalytic subunit (166 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna polymerase alpha subunit b (49 kDa, Protein from Homo sapiens)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8gwf
Q-score: 0.29
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Nsp (Complex)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_rna-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8gwg
Q-score: 0.007
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Protein from sars-cov-2 (Complex)
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- E-rtc_smp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8gwi
Q-score: 0.185
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- E-rtc_smp-nsp9_gtp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
- Rna (27-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 8gwn
Q-score: 0.407
Yan L, Huang Y, Ge J, Liu Z, Lu P, Huang B, Gao S, Wang J, Tan L, Ye S, Yu F, Lan W, Xu S, Zhou F, Shi L, Guddat LW, Gao Y, Rao Z, Lou Z
Cell (2022) 185 pp. 4347-4360.e17 [ Pubmed: 36335936 DOI: doi:10.1016/j.cell.2022.09.037 ]
- Non-structural protein 9 (12 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Primer (8 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Phosphoaminophosphonic acid-guanylate ester (522 Da, Ligand)
- E-rtc_atmp-nsp9_gmppnp (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (66 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)