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)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna (16 kDa, DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Centrin-2 (19 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)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- 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)
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 ]
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna (13 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (31 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (31 kDa, Protein from Homo sapiens)
- 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)
- Protein dna complex (610 kDa, Complex from Homo sapiens)
- Centrin-2 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (42 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (7 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (69 kDa, Protein from Homo sapiens)
- Dna (cy5) (13 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 4 (50 kDa, Protein from Homo sapiens)
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)
- Zinc ion (65 Da, Ligand)
- Bulky dna lesion recognition complex3 (Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Dna1 (7 kDa, DNA from synthetic construct)
- 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)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna (16 kDa, DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Centrin-2 (19 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)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Small dna lesion recognition complex1 (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Dna (ap) (16 kDa, DNA from synthetic construct)
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 ]
- Dna (ap) (16 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Dna (16 kDa, DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Centrin-2 (19 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)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- 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)
- Small dna lesion recognition complex2 (580 kDa, Complex from Homo sapiens)
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 (ap) (12 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (12 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex3 (610 kDa, Complex from Homo sapiens)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
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)
- Zinc ion (65 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 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 complex4 (440 kDa, Complex from Homo sapiens)
- Dna (7 kDa, DNA from synthetic construct)
- Dna (6 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6ukj
Q-score: 0.505
Kim J, Tan YZ, Wicht KJ, Erramilli SK, Dhingra SK, Okombo J, Vendome J, Hagenah LM, Giacometti SI, Warren AL, Nosol K, Roepe PD, Potter CS, Carragher B, Kossiakoff AA, Quick M, Fidock DA, Mancia F
Nature (2019) 576 pp. 315-320 [ Pubmed: 31776516 DOI: doi:10.1038/s41586-019-1795-x ]
- Fab light chain (23 kDa, Protein from Homo sapiens)
- Plasmodium falciparum chloroquine resistance transporter (pfcrt) (49 kDa, Cellular component from Plasmodium falciparum 7G8)
- Plasmodium falciparum chloroquine resistance transporter (pfcrt) 7g8 isoform complexed with fab (102 kDa, Cellular component)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Antigen-binding fragment (fab) (50 kDa, Cellular component from Homo sapiens)
- Chloroquine resistance transporter (53 kDa, Protein from Plasmodium falciparum (isolate 7G8))
- Fab heavy chain (25 kDa, Protein from Homo sapiens)