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 ]
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 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)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna (cy5) (16 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Bulky dna lesion recognition complex (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (46 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 ]
- General transcription factor iih subunit 4 (50 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (49 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)
- General transcription factor iih subunit 3 (31 kDa, Protein from Homo sapiens)
- Dna (cy5) (13 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih helicase subunit xpb (69 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (42 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)
- Dna (13 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (7 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 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 ]
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Dna1 (7 kDa, DNA from synthetic construct)
- 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)
- Zinc ion (65 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna2 (7 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
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 ]
- Dna repair protein complementing xp-c cells (107 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)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna (ap) (16 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 3 (34 kDa, Protein 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)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Small dna lesion recognition complex1 (580 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (46 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 ]
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 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)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Uv excision repair protein rad23 homolog b (44 kDa, Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna (ap) (16 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex2 (580 kDa, Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 2 (46 kDa, Protein 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 ]
- Xeroderma pigmentosum, complementation group c, isoform cra_a (107 kDa, Protein from Homo sapiens)
- Dna (ap) (12 kDa, DNA from synthetic construct)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- Dna (12 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Centrin-2 (19 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Small dna lesion recognition complex3 (610 kDa, Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- General transcription factor iih subunit 2 (46 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 ]
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- Small dna lesion recognition complex4 (440 kDa, Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (6 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Dna (7 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
CRISPR RNA-guided surveillance complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5u07
Q-score: 0.385
Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A
Cell (2017) 170 pp. 48-60.e11 [ DOI: doi:10.1016/j.cell.2017.06.012 Pubmed: 28666122 ]
- Crrna (19 kDa, RNA from Thermobifida fusca YX)
- Nontarget strand (3 kDa, DNA from Thermobifida fusca YX)
- Crispr rna-guided surveillance complex (Complex from Thermobifida fusca (strain YX))
- Cse2 (27 kDa, Protein from Thermobifida fusca YX)
- Crispr-associated protein, cse3 family (26 kDa, Protein from Thermobifida fusca YX)
- Target strand (6 kDa, DNA from Thermobifida fusca YX)
- Crispr-associated protein, cse1 family (61 kDa, Protein from Thermobifida fusca YX)
- Crispr-associated protein, cas5e family (28 kDa, Protein from Thermobifida fusca YX)
- Crispr-associated protein, cse4 family (41 kDa, Protein from Thermobifida fusca YX)
CRISPR RNA-guided surveillance complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 5u0a
Q-score: 0.443
Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A
Cell (2017) 170 pp. 48-60.e11 [ DOI: doi:10.1016/j.cell.2017.06.012 Pubmed: 28666122 ]
- Crispr-associated protein, cse3 family (26 kDa, Protein from Thermobifida fusca (strain YX))
- Crrna (19 kDa, RNA from Thermobifida fusca YX)
- Crispr-associated protein, cas5e family (28 kDa, Protein from Thermobifida fusca (strain YX))
- Crispr rna-guided surveillance complex (Complex from Thermobifida fusca (strain YX))
- Crispr-associated protein, cse4 family (41 kDa, Protein from Thermobifida fusca (strain YX))
- Nontarget strand (12 kDa, DNA from Thermobifida fusca YX)
- Target strand (15 kDa, DNA from Thermobifida fusca YX)
- Crispr-associated protein, cse1 family (61 kDa, Protein from Thermobifida fusca (strain YX))
- Cse2 (27 kDa, Protein from Thermobifida fusca (strain YX))
Structure of the STRA6 receptor for retinol uptake in complex with calmodulin
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 5sy1
Q-score: 0.38
Chen Y, Clarke OB, Kim J, Stowe S, Kim YK, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C, Blaner WS, Frank J, Quadro L, Weber DJ, Shapiro L, Hendrickson WA, Mancia F
Science (2016) 353 [ DOI: doi:10.1126/science.aad8266 Pubmed: 27563101 ]
- Stra6 (75 kDa, Protein from Danio rerio)
- Cholesterol (386 Da, Ligand)
- Calmodulin (16 kDa, Protein from Spodoptera frugiperda)
- Complex of zebrafish (d. rerio) stra6 with copurified calmodulin reconstituted in amphipol a8-35 (Complex from Danio rerio)
- Calcium ion (40 Da, Ligand)