Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8d97
Q-score: 0.407
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ Pubmed: 36007061 DOI: doi:10.1126/science.add5064 ]
- Ramp superfamily protein (184 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Rna (42-mer) (13 kDa, RNA from Candidatus Scalindua brodae)
- Apo gramp (Complex from Candidatus Scalindua brodae)
Resolution: 3.76 Å
EM Method: Single-particle
Fitted PDBs: 8d9e
Q-score: 0.416
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ Pubmed: 36007061 DOI: doi:10.1126/science.add5064 ]
- Rna (36-mer) (11 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein (143 kDa, Protein from Candidatus Scalindua brodae)
- Rna (5'-r(p*up*cp*cp*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*gp*up*a)-3') (6 kDa, RNA from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp-match pfs target (Complex from Candidatus Scalindua brodae)
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 8d9f
Q-score: 0.512
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ DOI: doi:10.1126/science.add5064 Pubmed: 36007061 ]
- Gramp-tpr-chat craspase (Complex from Candidatus Scalindua brodae)
- Rna (33-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Ramp superfamily protein (142 kDa, Protein from Candidatus Scalindua brodae)
- Chat domain protein (77 kDa, Protein from Candidatus Scalindua brodae)
gRAMP-TPR-CHAT Non match PFS target RNA(Craspase)
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8d9g
Q-score: 0.547
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ Pubmed: 36007061 DOI: doi:10.1126/science.add5064 ]
- Gramp-tpr-chat with non match pfs target rna craspase (Complex from Candidatus Scalindua brodae)
- Chat domain protein (78 kDa, Protein from Candidatus Scalindua brodae)
- Rna (5'-r(p*up*cp*cp*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*ap*cp*gp*ap*u)-3') (7 kDa, RNA from Candidatus Scalindua brodae)
- Rna (36-mer) (11 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein (147 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
gRAMP-TPR-CHAT match PFS target RNA(Craspase)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8d9h
Q-score: 0.426
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ Pubmed: 36007061 DOI: doi:10.1126/science.add5064 ]
- Rna (36-mer) (11 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (76 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp-tpr-chat with match pfs target rna craspase (Complex from Candidatus Scalindua brodae)
- Phosphate ion (94 Da, Ligand)
- Rna (5'-r(p*up*cp*cp*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*gp*u)-3') (6 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein (145 kDa, Protein from Candidatus Scalindua brodae)
gRAMP non-matching PFS-with Mg
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 8d9i
Q-score: 0.423
Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodriguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJJ, Ke A
Science (2022) 377 pp. 1278-1285 [ Pubmed: 36007061 DOI: doi:10.1126/science.add5064 ]
- Ramp superfamily protein (143 kDa, Protein from Candidatus Scalindua brodae)
- Rna (5'-r(p*up*cp*cp*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*a)-3') (6 kDa, RNA from Candidatus Scalindua brodae)
- Gramp-non matching pfs-with mg (Complex from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Rna (35-mer) (11 kDa, RNA from Candidatus Scalindua brodae)
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 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 4 (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)
- Dna repair protein complementing xp-a cells (Protein from Homo sapiens)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (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 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- 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 1 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Centrin-2 (Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpb (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 4, p52 (52 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 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)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- Dna (16 kDa, DNA from synthetic construct)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 1 (62 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 [ DOI: doi:10.1038/s41586-023-05959-z Pubmed: 37076618 ]
- General transcription factor iih subunit 4 (50 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (42 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (49 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (31 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Dna (13 kDa, DNA from synthetic construct)
- Dna repair protein complementing xp-a cells (20 kDa, Protein from Homo sapiens)
- Dna (cy5) (13 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpb (69 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpd (83 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Protein dna complex (610 kDa, Complex from Homo sapiens)
- Centrin-2 (8 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)