Yeast RAVE bound to V-ATPase V1 complex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9cop
Q-score: 0.252
Wang H, Tarsio M, Kane PM, Rubinstein JL
PNAS (2024) 121 pp. e2414511121-e2414511121 [ Pubmed: 39625975 DOI: doi:10.1073/pnas.2414511121 ]
- V-type proton atpase subunit f (13 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit e (26 kDa, Protein from Saccharomyces cerevisiae)
- Regulator of v-atpase in vacuolar membrane protein 2 (40 kDa, Protein from Saccharomyces cerevisiae)
- Suppressor of kinetochore protein 1 (22 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit h (54 kDa, Protein from Saccharomyces cerevisiae)
- Regulator of v-atpase in vacuolar membrane protein 1 (155 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit g (12 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase catalytic subunit a (118 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Yeast rave bound to v-atpase v1 complex (Complex from Saccharomyces cerevisiae)
- V-type proton atpase subunit b (57 kDa, Protein from Saccharomyces cerevisiae)
- V-type proton atpase subunit d (29 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 9chu
Q-score: 0.478
Xu J, Chen G, Wang H, Cao S, Heng J, Deupi X, Du Y, Kobilka BK
PNAS (2024) 121 pp. e2414544121-e2414544121 [ DOI: doi:10.1073/pnas.2414544121 Pubmed: 39565314 ]
- Calcineurin fused beta2ar in complex with fkbp12 (Complex)
- Fkbp1a (Complex from Homo sapiens)
- Calcineurin fused beta2ar (Complex from Homo sapiens)
- Protein phosphatase 3 catalytic subunit alpha (Complex from Mus musculus)
- Peptidyl-prolyl cis-trans isomerase fkbp1a (11 kDa, Protein from Homo sapiens)
- 8-deethyl-8-[but-3-enyl]-ascomycin (804 Da, Ligand)
- Noradrenaline (170 Da, Ligand)
- Beta-2 adrenergic receptor,calcineurin subunit b type 1 (49 kDa, Protein from Homo sapiens)
- Protein phosphatase 3 catalytic subunit alpha (42 kDa, Protein from Mus musculus)
cryo-EM structure of calcineurin-fused beta2 adrenergic receptor in apo state
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 9chv
Q-score: 0.39
Xu J, Chen G, Wang H, Cao S, Heng J, Deupi X, Du Y, Kobilka BK
PNAS (2024) 121 pp. e2414544121-e2414544121 [ DOI: doi:10.1073/pnas.2414544121 Pubmed: 39565314 ]
- Calcineurin fused beta2ar in complex with fkbp12 (Complex)
- Fkbp1a (Complex from Homo sapiens)
- Calcineurin fused beta2ar (Complex from Homo sapiens)
- Protein phosphatase 3 catalytic subunit alpha (Complex from Mus musculus)
- Beta-2 adrenergic receptor,calcineurin subunit b type 1 (51 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase fkbp1a (11 kDa, Protein from Homo sapiens)
- 8-deethyl-8-[but-3-enyl]-ascomycin (804 Da, Ligand)
- Protein phosphatase 3 catalytic subunit alpha (42 kDa, Protein from Mus musculus)
cryo-EM structure of calcineurin-fused beta2 adrenergic receptor in carazolol bound inactive state
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9chx
Q-score: 0.431
Xu J, Chen G, Wang H, Cao S, Heng J, Deupi X, Du Y, Kobilka BK
PNAS (2024) 121 pp. e2414544121-e2414544121 [ DOI: doi:10.1073/pnas.2414544121 Pubmed: 39565314 ]
- Calcineurin fused beta2ar in complex with fkbp12 (Complex)
- Fkbp1a (Complex from Homo sapiens)
- Calcineurin fused beta2ar (Complex from Homo sapiens)
- Protein phosphatase 3 catalytic subunit alpha (Complex from Mus musculus)
- (2s)-1-(9h-carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol (298 Da, Ligand)
- Beta-2 adrenergic receptor,calcineurin subunit b type 1 (51 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase fkbp1a (11 kDa, Protein from Homo sapiens)
- 8-deethyl-8-[but-3-enyl]-ascomycin (804 Da, Ligand)
- Protein phosphatase 3 catalytic subunit alpha (42 kDa, Protein from Mus musculus)
Structure of cobalamin-dependent methionine synthase (MetH) in a resting state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8g3h
Q-score: 0.303
Watkins MB, Wang H, Burnim A, Ando N
PNAS (2023) 120 pp. e2302531120-e2302531120 [ DOI: doi:10.1073/pnas.2302531120 Pubmed: 37339208 ]
- Methionine synthase (131 kDa, Protein from Thermus filiformis)
- Cobalamin-dependent methionine synthase holoprotein (132 kDa, Complex from Thermus filiformis)
- Cobalamin (1 kDa, Ligand)
- Zinc ion (65 Da, Ligand)
Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cen
Q-score: 0.269
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factors, and rna polymerase ii transcription factor b subunit 3 (Complex from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factors and mediator of rna polymerase ii transcription subunits (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunits (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator (2 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex from Synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 14 (84 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ceo
Q-score: 0.222
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator and the +1 nucleosome (2 MDa, Complex from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 isoform 1 (72 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (123 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Iron/sulfur cluster (351 Da, Ligand)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Toa1 isoform 1 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 6adl
Q-score: -0.025
Cao L, Zhang R, Liu T, Sun Z, Hu M, Sun Y, Cheng L, Guo Y, Fu S, Hu J, Li X, Yu C, Wang H, Chen H, Li X, Fry EE, Stuart DI, Qian P, Lou Z, Rao Z
PNAS (2018) 115 pp. 13087-13092 [ Pubmed: 30514821 DOI: doi:10.1073/pnas.1814309115 ]
- Vp1 (25 kDa, Protein from Senecavirus A)
- Vp3 (26 kDa, Protein from Senecavirus A)
- Anthrax toxin receptor 1 (21 kDa, Protein from Homo sapiens)
- Vp2 (27 kDa, Protein from Senecavirus A)
- Magnesium ion (24 Da, Ligand)
- Seneca valley virus (Virus from Seneca valley virus)
Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 6adm
Q-score: -0.027
Cao L, Zhang R, Liu T, Sun Z, Hu M, Sun Y, Cheng L, Guo Y, Fu S, Hu J, Li X, Yu C, Wang H, Chen H, Li X, Fry EE, Stuart DI, Qian P, Lou Z, Rao Z
PNAS (2018) 115 pp. 13087-13092 [ DOI: doi:10.1073/pnas.1814309115 Pubmed: 30514821 ]
- Vp2 (29 kDa, Protein from Seneca valley virus)
- Vp1 (28 kDa, Protein from Seneca valley virus)
- Seneca valley virus (Virus from Seneca valley virus)
- Vp4 (5 kDa, Protein from Seneca valley virus)
- Magnesium ion (24 Da, Ligand)
- Vp3 (26 kDa, Protein from Seneca valley virus)
- Anthrax toxin receptor 1 (21 kDa, Protein from Homo sapiens)
Anthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral conditions
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 6adr
Q-score: -0.016
Cao L, Zhang R, Liu T, Sun Z, Hu M, Sun Y, Cheng L, Guo Y, Fu S, Hu J, Li X, Yu C, Wang H, Chen H, Li X, Fry EE, Stuart DI, Qian P, Lou Z, Rao Z
PNAS (2018) 115 pp. 13087-13092 [ DOI: doi:10.1073/pnas.1814309115 Pubmed: 30514821 ]
- Water (18 Da, Ligand)
- Vp1 (28 kDa, Protein from Seneca valley virus)
- Vp2 (29 kDa, Protein from Seneca valley virus)
- Vp4 (7 kDa, Protein from Seneca valley virus)
- Vp3 (26 kDa, Protein from Seneca valley virus)
- Seneca valley virus (Virus from Seneca valley virus)
- Magnesium ion (24 Da, Ligand)
- Anthrax toxin receptor 1 (21 kDa, Protein from Homo sapiens)