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 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- 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)
- General transcription and dna repair factor iih helicase subunit xpb (69 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Protein dna complex (610 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (42 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (20 kDa, Protein from Homo sapiens)
- Dna (cy5) (13 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (31 kDa, Protein from Homo sapiens)
- Dna (13 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 3 (31 kDa, Protein from Homo sapiens)
- Centrin-2 (8 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)
- 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 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna (ap) (16 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- Dna (16 kDa, DNA from synthetic construct)
- 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)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex1 (580 kDa, Complex from Homo sapiens)
- 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)
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)
DNA-PK complex of DNA end processing
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7sgl
Q-score: 0.445
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Hairpin_1 (16 kDa, DNA from synthetic construct)
- Inositol hexakisphosphate (660 Da, Ligand)
- X-ray repair cross-complementing protein 6 (70 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Complex of dna-pkcs, ku70, ku80, artemis and dna (720 kDa, Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
- Protein artemis (79 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
CryoEM structure of DNA-PK complex VII
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7su3
Q-score: 0.528
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- X-ray repair cross-complementing protein 6 (69 kDa, Protein from Homo sapiens)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Dna-pk complex vii (Complex)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Dna (5'-d(*ap*ap*gp*cp*ap*gp*tp*ap*gp*ap*g)-3') (4 kDa, DNA from Escherichia coli)
- Dna (5'-d(*gp*cp*ap*tp*gp*cp*tp*cp*tp*ap*cp*tp*gp*cp*tp*tp*cp*gp*ap*tp*ap*tp*cp*g)-3') (7 kDa, DNA from Escherichia coli)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)
CryoEM structure of DNA-PK complex VIII
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7sud
Q-score: 0.403
Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M
Mol Cell (2022) 82 pp. 177- [ Pubmed: 34936881 DOI: doi:10.1016/j.molcel.2021.11.025 ]
- Dna-pk (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna-dependent protein kinase catalytic subunit (469 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- X-ray repair cross-complementing protein 5 (82 kDa, Protein from Homo sapiens)