Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 2
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8z8j
Q-score: 0.515
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Cryo-em structure of thogoto virus polymerase in transcription pre-initiation conformation 2 (Complex from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
Cryo-EM structure of Thogoto virus polymerase in a transcription initiation conformation
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8z8x
Q-score: 0.525
Xue L, Chang T, Li Z, Wang C, Zhao H, Li M, Tang P, Wen X, Yu M, Wu J, Bao X, Wang X, Gong P, He J, Chen X, Xiong X
Nat Commun (2024) 15 pp. 4620-4620 [ DOI: doi:10.1038/s41467-024-48848-3 Pubmed: 38816392 ]
- Cryo-em structure of thogoto virus polymerase in a transcription initiation conformation (Complex from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*gp*ap*cp*up*gp*cp*cp*up*gp*up*up*up*up*up*gp*cp*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna (5'-r(*ap*gp*ap*gp*ap*ap*ap*up*cp*ap*ap*gp*gp*cp*ap*gp*up*u)-3') (5 kDa, RNA from Thogoto virus (isolate SiAr 126))
- Rna-directed rna polymerase catalytic subunit (81 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase acidic protein (71 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Polymerase basic protein 2 (94 kDa, Protein from Thogoto virus (isolate SiAr 126))
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Local CryoEM structure of the SARS-CoV-2 S6P in complex with 7B3 Fab
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8i3s
Q-score: 0.4
Liu Q, Zhao H, Li Z, Zhang Z, Huang R, Gu M, Zhuang K, Xiong Q, Chen X, Yu W, Qian S, Zhang Y, Tan X, Zhang M, Yu F, Guo M, Huang Z, Wang X, Xiang W, Wu B, Mei F, Cai K, Zhou L, Zhou L, Wu Y, Yan H, Cao S, Lan K, Chen Y
Signal Transduct Target Ther (2023) 8 pp. 347-347 [ DOI: doi:10.1038/s41392-023-01615-0 Pubmed: 37704615 ]
- Heavy chain od fab 7b3 (24 kDa, Protein from Homo sapiens)
- Spike-fab complex (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of fab 7b3 (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Local CryoEM structure of the SARS-CoV-2 S6P in complex with 14B1 Fab
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8i3u
Q-score: 0.462
Liu Q, Zhao H, Li Z, Zhang Z, Huang R, Gu M, Zhuang K, Xiong Q, Chen X, Yu W, Qian S, Zhang Y, Tan X, Zhang M, Yu F, Guo M, Huang Z, Wang X, Xiang W, Wu B, Mei F, Cai K, Zhou L, Zhou L, Wu Y, Yan H, Cao S, Lan K, Chen Y
Signal Transduct Target Ther (2023) 8 pp. 347-347 [ DOI: doi:10.1038/s41392-023-01615-0 Pubmed: 37704615 ]
- Heavy chain of fab 14b1 (16 kDa, Protein from Homo sapiens)
- Light chain of fab 14b1 (14 kDa, Protein from Homo sapiens)
- Spike-fab complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.88 Å
EM Method: Single-particle
Fitted PDBs: 7wp8
Q-score: 0.441
Wu Y, Wang S, Zhang Y, Yuan L, Zheng Q, Wei M, Shi Y, Wang Z, Ma J, Wang K, Nie M, Xiao J, Huang Z, Chen P, Guo H, Lan M, Xu J, Hou W, Hong Y, Chen D, Sun H, Xiong H, Zhou M, Liu C, Guo W, Guo H, Gao J, Gan C, Li Z, Zhang H, Wang X, Li S, Cheng T, Zhao Q, Chen Y, Wu T, Zhang T, Zhang J, Cao H, Zhu H, Yuan Q, Guan Y, Xia N
Cell Host Microbe (2022) 30 pp. 1732-1744.e7 [ Pubmed: 36323313 DOI: doi:10.1016/j.chom.2022.10.011 ]
- 83h7 heavy chain (13 kDa, Protein from Mus musculus)
- Cryo-em structure of sars-cov-2 recombinant spike protein stfk1628x in complex with three neutralizing antibodies (Complex from Mus musculus)
- Neutralizing antibodies (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2b4 light chain (12 kDa, Protein from Mus musculus)
- Spike protein stfk1628x (Complex)
- 85f7 heavy chain (13 kDa, Protein from Mus musculus)
- 85f7 light chain (11 kDa, Protein from Mus musculus)
- 83h7 light chain (11 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (20 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2b4 heavy chain (13 kDa, Protein from Mus musculus)
Resolution: 3.81 Å
EM Method: Single-particle
Fitted PDBs: 7wp6
Q-score: 0.438
Wu Y, Wang S, Zhang Y, Yuan L, Zheng Q, Wei M, Shi Y, Wang Z, Ma J, Wang K, Nie M, Xiao J, Huang Z, Chen P, Guo H, Lan M, Xu J, Hou W, Hong Y, Chen D, Sun H, Xiong H, Zhou M, Liu C, Guo W, Guo H, Gao J, Gan C, Li Z, Zhang H, Wang X, Li S, Cheng T, Zhao Q, Chen Y, Wu T, Zhang T, Zhang J, Cao H, Zhu H, Yuan Q, Guan Y, Xia N
Cell Host Microbe (2022) 30 pp. 1732-1744.e7 [ Pubmed: 36323313 DOI: doi:10.1016/j.chom.2022.10.011 ]
- 83h7 heavy chain (13 kDa, Protein from Mus musculus)
- 36h6 light chain (12 kDa, Protein from Mus musculus)
- Spike protein stfk (Complex)
- Neutralizing antibodies (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 85f7 heavy chain (13 kDa, Protein from Mus musculus)
- 85f7 light chain (11 kDa, Protein from Mus musculus)
- 36h6 heavy chain (13 kDa, Protein from Mus musculus)
- 83h7 light chain (11 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of sars-cov-2 recombinant spike protein stfk in complex with three neutralizing antibodies (Complex from Mus musculus)
p53-bound TFIID-based holo PIC on HDM2 promoter
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7egc
Q-score: 0.051
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- P53-bound tfiid-based holo pic on hdm2 promoter (Complex)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna(hdm2 promoters) (Complex)
- Tfiia (Complex from Homo sapiens)
- Dna (71-mer) (22 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tfiih (Complex)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Dna (71-mer) (21 kDa, DNA from Homo sapiens)
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 7egh
Q-score: 0.481
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- Tfiid lobe c subcomplex (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna (45-mer) (22 kDa, DNA from Homo sapiens)
- Dna (45-mer) (28 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
TFIID-based intermediate PIC on SCP promoter
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7eg9
Q-score: 0.137
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Dna (79-mer) (24 kDa, DNA from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna (79-mer) (24 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Tfiie (Complex)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna(scp promoters) (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Tfiid-based intermediate pic on scp promoter (Complex)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
TFIID-based holo PIC on SCP promoter
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7egb
Q-score: 0.012
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ Pubmed: 33795473 DOI: doi:10.1126/science.aba8490 ]
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Tfiid-based holo pic on scp promoter (Complex)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna(scp promoters) (Complex)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Tfiia (Complex from Homo sapiens)
- Dna (69-mer) (29 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Dna (69-mer) (21 kDa, DNA from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Tfiih (Complex)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)