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Molecular architecture of the chikungunya virus replication complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7y38
Q-score: 0.539
Tan YB, Chmielewski D, Law MCY, Zhang K, He Y, Chen M, Jin J, Luo D
Sci Adv (2022) 8 pp. eadd2536-eadd2536 [ Pubmed: 36449616 DOI: doi:10.1126/sciadv.add2536 ]
- Nsp2 helicase-protease; docked on top of viral complex with synthetic rna bound (Complex from Chikungunya virus strain S27-African prototype)
- Nsp1 dodecameric ring (Complex from Chikungunya virus strain S27-African prototype)
- Nsp4 rdrp; docked within nsp1 central cavity (Complex from Onyong-nyong virus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Rna-directed rna polymerase nsp4 (68 kDa, Protein from Onyong-nyong virus)
- Protease nsp2 (89 kDa, Protein from Chikungunya virus strain S27-African prototype)
- Rna (5'-r(p*cp*cp*a)-3') (894 Da, RNA from in vitro transcription vector pT7-TP(deltai))
- Zinc ion (65 Da, Ligand)
- Alphavirus replication complex (100 kDa, Complex)
- Mrna-capping enzyme nsp1,affinity-tag (strepii-3xflag) (64 kDa, Protein from Chikungunya virus strain S27-African prototype)
Cryo-EM structure of HK022 putRNA-associated E.coli RNA polymerase elongation complex
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 7xue
Q-score: 0.476
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Dna/rna (Complex)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Hk022 putrna-associated e.coli rna polymerase elongation complex (440 kDa, Complex)
- Rna polymerase (Complex from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Rna (nun gene and immunity region) (30 kDa, RNA from Shamshuipovirus HK022)
- Zinc ion (65 Da, Ligand)
cryo-EM structure of HK022 putRNA-less E.coli RNA polymerase elongation complex
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7xug
Q-score: 0.446
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Dna/rna (Complex)
- E.coli rna polymerase (Complex from Escherichia coli (strain K12))
- Magnesium ion (24 Da, Ligand)
- Non-template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Hk022 putrna-less e.coli rna polymerase elongation complex (440 kDa, Complex)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Rna (nun gene and immunity region) (30 kDa, RNA from Shamshuipovirus HK022)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 7xui
Q-score: 0.416
Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY
Nat Commun (2022) 13 pp. 4668-4668 [ Pubmed: 35970830 DOI: doi:10.1038/s41467-022-32315-y ]
- Dna/rna (Complex)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rna (122-mer) (39 kDa, RNA from Shamshuipovirus HK022)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Sigma70 bound hk022 putrna-associated e.coli rna polymerase elongation complex (510 kDa, Complex)
- Rna polymerase (Complex from Escherichia coli (strain K12))
- Template dna (54 kDa, DNA from Shamshuipovirus HK022)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
Structure of the post state human RNA Polymerase I Elongation Complex
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 7vbb
Q-score: 0.401
Zhao D, Liu W, Chen K, Wu Z, Yang H, Xu Y
Cell Discov (2021) 7 pp. 97-97 [ Pubmed: 34671025 DOI: doi:10.1038/s41421-021-00335-5 ]
- Dna (25-mer) (7 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna (5'-d(*cp*tp*gp*tp*cp*cp*tp*cp*tp*gp*gp*cp*gp*a)-3') (4 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa1 (194 kDa, Protein from Homo sapiens)
- Post state of human rna polymerase i elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa34 (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa43 (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*cp*up*gp*ap*cp*u)-3') (2 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa49 (47 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa2 (128 kDa, Protein from Homo sapiens)
Structure of the pre state human RNA Polymerase I Elongation Complex
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 7vba
Q-score: 0.525
Zhao D, Liu W, Chen K, Wu Z, Yang H, Xu Y
Cell Discov (2021) 7 pp. 97-97 [ Pubmed: 34671025 DOI: doi:10.1038/s41421-021-00335-5 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Human rna polymerase i elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*a*cp*tp*gp*tp*cp*cp*tp*cp*tp*gp*gp*c)-3') (3 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa1 (194 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*gp*cp*cp*ap*gp*ap*gp*ap*cp*ap*gp*cp*gp*ap*gp*tp*cp*ap*gp*cp*ap*a)-3') (6 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa34 (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa43 (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*cp*up*gp*ap*cp*u)-3') (2 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa49 (47 kDa, Protein from Homo sapiens)
- 5'-o-[(s)-hydroxy{[(s)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (481 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa2 (128 kDa, Protein from Homo sapiens)
Back track state of human RNA Polymerase I Elongation Complex
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 7vbc
Q-score: 0.373
Zhao D, Liu W, Chen K, Wu Z, Yang H, Xu Y
Cell Discov (2021) 7 pp. 97-97 [ Pubmed: 34671025 DOI: doi:10.1038/s41421-021-00335-5 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna (5'-d(*gp*tp*ap*cp*tp*gp*tp*cp*cp*tp*cp*tp*gp*g)-3') (4 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa1 (194 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa34 (55 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*ap*gp*gp*ap*cp*ap*gp*cp*gp*tp*gp*tp*cp*ap*gp*cp*ap*ap*tp*a)-3') (6 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa43 (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*cp*up*gp*a)-3') (1 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase i subunit rpa49 (47 kDa, Protein from Homo sapiens)
- Back track state of human rna polymerase i elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa2 (128 kDa, Protein from Homo sapiens)
The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 7eu0
Q-score: 0.487
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ Pubmed: 34941388 DOI: doi:10.1126/science.abj9184 ]
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Mouse-ear cress)
- Dna (33-mer) (9 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from thale cress)
- A. thaliana pol iv-rdr2 backtracked complex (550 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from thale cress)
- Dna (5'-d(*cp*tp*gp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*gp*ap*gp*tp*g)-3') (6 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from thale cress)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from thale cress)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from thale cress)
- Magnesium ion (24 Da, Ligand)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from thale cress)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from thale cress)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from thale cress)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from thale cress)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from thale cress)
- Rna (39-mer) (12 kDa, RNA from synthetic construct)
Cryo-EM structure of human RNA Polymerase I in elongation state
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ob9
Q-score: 0.519
Misiaszek AD, Girbig M, Grotsch H, Baudin F, Murciano B, Lafita A, Muller CW
Nat Struct Mol Biol (2021) 28 pp. 997-1008 [ Pubmed: 34887565 DOI: doi:10.1038/s41594-021-00693-4 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Human)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Human)
- Rna polymerase i (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Human)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Human)
- Dna-directed rna polymerase i subunit rpa1 (195 kDa, Protein from Human)
- Dna-directed rna polymerase i subunit rpa34 (55 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Human)
- Dna template strand (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa49 (47 kDa, Protein from Human)
- Dna non-template strand (13 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Human)
- Dna-directed rna polymerase i subunit rpa2 (128 kDa, Protein from Human)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Human)
- Magnesium ion (24 Da, Ligand)
- Rna and dna (Complex from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa43 (37 kDa, Protein from Human)
- Rna (9 kDa, RNA from Homo sapiens)
- Rna polymerase i (Complex)
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC dimer
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7re3
Q-score: 0.321
Chen J, Wang Q, Malone B, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE, Darst SA
Nat Struct Mol Biol (2022) 29 pp. 250-260 [ DOI: doi:10.1038/s41594-022-00734-6 Pubmed: 35260847 ]
- Non-structural protein 8 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Rna-directed rna polymerase (106 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-rtc dimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Helicase (67 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Template rna (17 kDa, RNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Aluminum fluoride (83 Da, Ligand)
- Product rna (11 kDa, RNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Chapso (631 Da, Ligand)