Bulky DNA lesion recognition complex 3
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 3 (440 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH focused
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Bulky dna lesion recognition complex 1 (270 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Centrin-2 (Protein from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8ebs
Q-score: 0.274
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna (16 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8ebt
Q-score: 0.304
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- Protein dna complex (610 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (42 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (50 kDa, Protein from Homo sapiens)
- Dna (cy5) (13 kDa, DNA from synthetic construct)
- Dna (13 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna repair protein complementing xp-a cells (20 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (83 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (7 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (49 kDa, Protein from Homo sapiens)
- Centrin-2 (8 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (69 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
XPC release from Core7-XPA-DNA (Cy5)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ebu
Q-score: 0.341
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna1 (7 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex3 (Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Dna2 (7 kDa, DNA from synthetic construct)
Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1
Resolution: 7.1 Å
EM Method: Single-particle
Fitted PDBs: 8ebv
Q-score: 0.16
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Dna (ap) (16 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex1 (580 kDa, Complex from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna (16 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Initial DNA-lesion (AP) binding by XPC and TFIIH complex2
Resolution: 5.6 Å
EM Method: Single-particle
Fitted PDBs: 8ebw
Q-score: 0.208
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (ap) (16 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex2 (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna (16 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ebx
Q-score: 0.262
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Dna (12 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Dna (ap) (12 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex3 (610 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
XPC release from Core7-XPA-DNA (AP)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8eby
Q-score: 0.3
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Dna (7 kDa, DNA from synthetic construct)
- Small dna lesion recognition complex4 (440 kDa, Complex from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- Dna (6 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
SARS-COV-2 Spike RBDMACSp6 binding to hACE2
Resolution: 3.69 Å
EM Method: Single-particle
Fitted PDBs: 7fdg
Q-score: 0.364
Sun S, Gu H, Cao L, Chen Q, Ye Q, Yang G, Li RT, Fan H, Deng YQ, Song X, Qi Y, Li M, Lan J, Feng R, Guo Y, Zhu N, Qin S, Wang L, Zhang YF, Zhou C, Zhao L, Chen Y, Shen M, Cui Y, Yang X, Wang X, Tan W, Wang H, Wang X, Qin CF
Nat Commun (2021) 12 pp. 5654-5654 [ Pubmed: 34580297 DOI: doi:10.1038/s41467-021-25903-x ]
- Sars-cov-2 spike rbdmacsp6-hace2 complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (24 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (71 kDa, Protein from Homo sapiens)