Cryo-EM structure of the human TRPC5 ion channel in complex with G alpha i3 subunits, class1
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7x6i
Q-score: 0.392
Won J, Kim J, Jeong H, Kim J, Feng S, Jeong B, Kwak M, Ko J, Im W, So I, Lee HH
Nat Commun (2023) 14 pp. 2550-2550 [ Pubmed: 37137991 DOI: doi:10.1038/s41467-023-38281-3 ]
- Zinc ion (65 Da, Ligand)
- Trp channel (Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- (2s)-2-(hexadecanoyloxy)-3-hydroxypropyl (9z)-octadec-9-enoate (594 Da, Ligand)
- G protein (Complex)
- Phosphatidylethanolamine (734 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-3 (41 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Trp channel-g protein complex (Complex from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Short transient receptor potential channel 5 (89 kDa, 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)
- 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)
Complex structure of Neuropeptide Y Y2 receptor in complex with PYY(3-36) and Gi
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 7yon
Q-score: 0.572
Kang H, Park C, Choi YK, Bae J, Kwon S, Kim J, Choi C, Seok C, Im W, Choi HJ
Structure (2023) 31 pp. 44-57.e6 [ Pubmed: 36525977 DOI: doi:10.1016/j.str.2022.11.010 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Pyy(3-36) (Complex)
- Neuropeptide y receptor type 2 (43 kDa, Protein from Homo sapiens)
- Peptide yy(3-36) (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein (Complex)
- Complex structure of pyy(3-36)-y2r-gi-scfv16 (Complex from Homo sapiens)
- Single-chain antibody fv fragment (scfv16) (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Mus musculus)
- Water (18 Da, Ligand)
Complex structure of Neuropeptide Y Y2 receptor in complex with NPY and Gi
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7yoo
Q-score: 0.531
Kang H, Park C, Choi YK, Bae J, Kwon S, Kim J, Choi C, Seok C, Im W, Choi HJ
Structure (2023) 31 pp. 44-57.e6 [ Pubmed: 36525977 DOI: doi:10.1016/j.str.2022.11.010 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Npy (Complex)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Neuropeptide y (4 kDa, Protein from Homo sapiens)
- Scfv16 (Complex)
- Neuropeptide y receptor type 2 (43 kDa, Protein from Homo sapiens)
- Complex structure of npy-y2r-gi-scfv16 (Complex from Homo sapiens)
- Single-chain antibody fv fragment (scfv16) (27 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein (Complex from Mus musculus)