The cryo-EM structure of PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8szk
Q-score: 0.327
Hu Y, Delviks-Frankenberry KA, Wu C, Arizaga F, Pathak VK, Xiong Y
Nat Struct Mol Biol (2024) 31 pp. 1492-1501 [ Pubmed: 38789685 DOI: doi:10.1038/s41594-024-01314-6 ]
- Ppp2r5a in complex with hiv-1 vif/cbfb/elob/eloc (Complex from Homo sapiens)
- Virion infectivity factor (20 kDa, Protein from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Serine/threonine-protein phosphatase 2a 56 kda regulatory subunit alpha isoform (56 kDa, Protein from Homo sapiens)
- Core-binding factor subunit beta (23 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 8fvi
Q-score: 0.431
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Dna dc->du-editing enzyme apobec-3h (22 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Rna(5'-r(*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (2 kDa, RNA from Escherichia coli)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
- Hetero-hexameric complex of hiv-1 vif and human apobec3h, cbf-beta, elob, eloc, and cul5 (120 kDa, Complex from Homo sapiens)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Rna(5'-r(ap*up*up*up*up*up*up*up*up*u)-3') (3 kDa, RNA from Escherichia coli)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Elongin-b (11 kDa, Protein from Homo sapiens)
- Cullin 5 (36 kDa, Protein from Homo sapiens)
Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8fvj
Q-score: 0.374
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Dimeric form of hiv-1 vif in complex with human cbf-beta, elob, eloc, and cul5 (198 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
- Cullin-5 (36 kDa, Protein from Homo sapiens)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Elongin-b (11 kDa, Protein from Homo sapiens)
HIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
Nat Commun (2023) 14 pp. 5241-5241 [ DOI: doi:10.1038/s41467-023-40955-x Pubmed: 37640699 ]
- Core-binding factor subunit beta (Protein from Homo sapiens)
- Ring-box protein 2 (Protein from Homo sapiens)
- Dna dc->du-editing enzyme apobec-3h (Protein from Homo sapiens)
- Virion infectivity factor (Protein from Human immunodeficiency virus 1)
- Elongin-b (Protein from Homo sapiens)
- Hetero-heptameric complex of hiv-1 vif and human apobec3h, cbf-beta, elob, eloc, cul5, and rbx2 (Complex from Homo sapiens)
- Elongin-c (Protein from Homo sapiens)
- Cullin-5 (Protein from Homo sapiens)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8cx0
Q-score: 0.509
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Zinc ion (65 Da, Ligand)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*ap*ap*ap*ap*ap*a)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8cx1
Q-score: 0.366
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*up*ap*ap*ap*up*ap*up*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*ap*ap*ap*up*ap*up*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8cx2
Q-score: 0.375
Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD
Nature (2023) 615 pp. 728-733 [ Pubmed: 36754086 DOI: doi:10.1038/s41586-023-05779-1 ]
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*ap*ap*up*ap*ap*ap*ap*ap*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Hiv-1 vif-e3 ligase substrate receptor (vcbc) in complex with human apobec3g and rna (Complex from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Virion infectivity factor (22 kDa, Protein from Human immunodeficiency virus 1)
- Core-binding factor subunit beta (21 kDa, Protein from Homo sapiens)
- Dna dc->du-editing enzyme apobec-3g (50 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*up*up*ap*ap*ap*ap*ap*u)-3') (2 kDa, RNA from Spodoptera frugiperda)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7upn
Q-score: 0.402
Hu Y, Gudnadottir RB, Knecht KM, Arizaga F, Jonsson SR, Xiong Y
Sci Adv (2023) 9 pp. eadd3422-eadd3422 [ DOI: doi:10.1126/sciadv.add3422 Pubmed: 36638173 ]
- Maedi visna virus vif in complex with human cypa and elongin bc components of e3 ubiquitin ligase (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Peptidyl-prolyl cis-trans isomerase a (18 kDa, Protein from Homo sapiens)
- Virion infectivity factor (28 kDa, Protein from Visna-maedi virus)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8e40
Q-score: 0.343
Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS
Sci Adv (2023) 9 pp. eade3168-eade3168 [ DOI: doi:10.1126/sciadv.ade3168 Pubmed: 36598981 ]
- Zinc ion (65 Da, Ligand)
- Core-binding factor subunit beta (18 kDa, Protein from Homo sapiens)
- Rna (8 kDa, RNA from Escherichia coli)
- Virion infectivity factor (21 kDa, Protein from Human immunodeficiency virus 1)
- Complex of apobec3g with hiv-1 vif and cbf-beta bound to fork rna (99 kDa, Complex from Human immunodeficiency virus 1)
- Dna dc->du-editing enzyme apobec-3g (45 kDa, Protein from Macaca mulatta)
- Rna (6 kDa, RNA from Escherichia coli)
APOBEC3G in complex with HIV-1 Vif/CBF-beta/EloB/EloC/Cul5/Rbx2
Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS
Sci Adv (2023) 9 pp. eade3168-eade3168 [ DOI: doi:10.1126/sciadv.ade3168 Pubmed: 36598981 ]
- Core-binding factor subunit beta (Protein from Homo sapiens)
- Apobec3g (Protein from Macaca mulatta)
- Complex of apobec3g with hiv-1 vif, cbf-beta, elongin-b, elongin-c, cullin-5, and ring-box protein 2 (210 kDa, Complex from Human immunodeficiency virus 1)
- Ring-box protein 2 (Protein from Homo sapiens)
- Virion infectivity factor (Protein from Human immunodeficiency virus 1)
- Elongin-b (Protein from Homo sapiens)
- Elongin-c (Protein from Homo sapiens)
- Cullin-5 (Protein from Homo sapiens)