Cryo-EM structure of the SV1-Gs complex.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7v9l
Q-score: 0.505
Cong Z, Zhou F, Zhang C, Zou X, Zhang H, Wang Y, Zhou Q, Cai X, Liu Q, Li J, Shao L, Mao C, Wang X, Wu J, Xia T, Zhao LH, Jiang H, Zhang Y, Xu HE, Cheng X, Yang D, Wang MW
PNAS (2021) 118 [ Pubmed: 34599099 DOI: doi:10.1073/pnas.2106606118 ]
- Nanobody 35 (15 kDa, Protein from synthetic construct)
- Cryo-em structure of the human growth hormone releasing hormone receptor splice variant 1 in complex with g protein (Complex from Homo sapiens)
- Ghrh receptor splice variant 1,ghrh receptor splice variant 1,ghrh receptor splice variant 1,sv1 (57 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (41 kDa, Protein from Homo sapiens)
TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
Resolution: 4.07 Å
EM Method: Single-particle
Fitted PDBs: 7ena
Q-score: 0.168
Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y
Science (2021) 372 [ DOI: doi:10.1126/science.abg0635 Pubmed: 33958484 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Mediator (Complex from Homo sapiens)
- Tfiid (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Tfiif (Complex from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Dna(69-mer) (21 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Dna (69-mer) (21 kDa, DNA from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase (Complex)
- Tfiid-based pic-mediator holo-complex in pre-assembled state (pre-hpic-med) (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Rpb1 (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Tfiia-a (34 kDa, Protein from Homo sapiens)
- Tfiih (Complex from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
p53-bound TFIID-based holo PIC on HDM2 promoter
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7egc
Q-score: 0.051
Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y
Science (2021) 372 [ DOI: doi:10.1126/science.aba8490 Pubmed: 33795473 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- P53-bound tfiid-based holo pic on hdm2 promoter (Complex)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Tfiih (Complex)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Dna(hdm2 promoters) (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna (71-mer) (21 kDa, DNA from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (71-mer) (22 kDa, DNA from Homo sapiens)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Rpb10 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Tfiid (Complex from Homo sapiens)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7emf
Q-score: 0.331
Chen X, Yin X, Li J, Wu Z, Qi Y, Wang X, Liu W, Xu Y
Science (2021) 372 [ DOI: doi:10.1126/science.abg0635 Pubmed: 33958484 ]
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Structure of the human mediator complex (Complex from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- Unknown chain (poly a) (1 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
The atomic structure of a human adeno-associated virus capsid isolate (AAVhu69/AAVv66)
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 6u3q
Q-score: 0.63
Hsu HL, Brown A, Loveland AB, Lotun A, Xu M, Luo L, Xu G, Li J, Ren L, Su Q, Gessler DJ, Wei Y, Tai PWL, Korostelev AA, Gao G
Nat Commun (2020) 11 pp. 3279-3279 [ Pubmed: 32606306 DOI: doi:10.1038/s41467-020-17047-1 ]
- Adeno-associated virus (Virus from Adeno-associated virus)
- Capsid protein vp1 (81 kDa, Protein from Adeno-associated virus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7bvg
Q-score: 0.537
Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z
Science (2020) 368 pp. 1211-1219 [ DOI: doi:10.1126/science.aba9102 Pubmed: 32327601 ]
- Phosphate ion (94 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Integral membrane indolylacetylinositol arabinosyltransferase embb (119 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- [(2z,6e,10e,14z,18e,22z,26z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2s,3s,4s,5r)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate (911 Da, Ligand)
- Emba and embb (Complex from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis arabinosyltransferase emba-embb-acpm2 in complex with di-arabinose (Complex)
- Acpm (Complex from Mycolicibacterium smegmatis MC2 155)
- 4'-phosphopantetheine (358 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Integral membrane indolylacetylinositol arabinosyltransferase emba (116 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Meromycolate extension acyl carrier protein (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6m71
Q-score: 0.519
Gao Y, Yan L, Huang Y, Liu F, Zhao Y, Cao L, Wang T, Sun Q, Ming Z, Zhang L, Ge J, Zheng L, Zhang Y, Wang H, Zhu Y, Zhu C, Hu T, Hua T, Zhang B, Yang X, Li J, Yang H, Liu Z, Xu W, Guddat LW, Wang Q, Lou Z, Rao Z
Science (2020) 368 pp. 779-782 [ Pubmed: 32277040 DOI: doi:10.1126/science.abb7498 ]
- Rna-directed rna polymerase (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (9 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 rna-dependent rna polymerase in complex with cofactors (155 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6adq
Q-score: 0.458
Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z
Science (2018) 362 [ DOI: doi:10.1126/science.aat8923 Pubmed: 30361386 ]
- Palmitic acid (256 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Ubiquinol-cytochrome c reductase cytochrome b subunit (60 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Lpqe protein (19 kDa, Protein from Mycobacterium smegmatis MC2 51)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Superoxide dismutase in complex with bcc-aa3 type ciii-civ supercomplex from mycobacterium smegmatis (800 kDa, Complex from Mycobacterium smegmatis MC2 51)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Heme c (618 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (30 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Rieske iron-sulfur protein qcra (46 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Copper (ii) ion (63 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycobacterium smegmatis MC2 51)