8FVJ: Dimeric form of HIV-1 Vif

Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5. Determined by electron microscopy at 3.54 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 10
Atoms: 12,562
Mol. weight: 197.63 kDa
Ligands: ZN
Released: 6 Sept 2023

Explore 8FVJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FVJ contains 76 α-helices and 63 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-21	6
β-strand	25-27	3	1
α-helix	37-48	12
β-strand	55-57	3	2
β-strand	64-65	2	3
β-strand	66-69	4	2
β-strand	87	1	3
β-strand	98-103	6	3
β-strand	106-111	6	3
β-strand	114-115	2	1
β-strand	120-123	4	1
β-strand	125-127	3	3
α-helix	129-134	6
α-helix	137-148	12

Chains 1 and 6: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	2
β-strand	10-13	4	3
α-helix	15-30	16
β-strand	41	1	3
β-strand	51-57	7	3
β-strand	63-69	7	3
β-strand	83-90	8	3
β-strand	95-97	3	3
α-helix	100-108	9
α-helix	117-119	3
α-helix	121-124	4
α-helix	136-138	3
α-helix	146-154	9
α-helix	168-171	4

Chain 2: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	15-30	16
α-helix	37-53	17
α-helix	57-82	26
α-helix	86-106	21
α-helix	112-117	6
α-helix	134-143	10
α-helix	144-148	5
α-helix	149-168	20
α-helix	174-186	13
α-helix	196-198	3
α-helix	199-203	5
α-helix	204-224	21
α-helix	228-247	20
α-helix	258-269	12
α-helix	274-287	14
α-helix	290-299	10
α-helix	307-318	12

Chain 3: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	4
β-strand	9	1	5
β-strand	10	1	6
β-strand	12	1	5
β-strand	15	1	4
α-helix	24-26	3
α-helix	27-31	5
α-helix	33-35	3
β-strand	43-44	2	7
α-helix	57-60	4
β-strand	68	1	8
β-strand	71	1	8
β-strand	74	1	4
β-strand	77-78	2	7
β-strand	90	1	6
α-helix	91-94	4

Chains 4 and 9: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	9
β-strand	21-22	2	5
β-strand	28	1	5
β-strand	31	1	9
α-helix	33-36	4
α-helix	40-46	7
β-strand	60-61	2	5
α-helix	67-82	16
α-helix	100-109	10

Chain 5: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-21	6
β-strand	25-27	3	10
α-helix	37-48	12
β-strand	55-57	3	11
β-strand	64-65	2	12
β-strand	66-69	4	11
β-strand	98-103	6	12
β-strand	106-111	6	12
β-strand	114-115	2	10
β-strand	120-123	4	10
β-strand	125-127	3	12
α-helix	129-134	6
α-helix	137-148	12

Chain 7: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	15-30	16
α-helix	37-53	17
α-helix	57-82	26
α-helix	86-106	21
α-helix	112-117	6
α-helix	134-143	10
α-helix	144-148	5
α-helix	149-168	20
α-helix	174-186	13
α-helix	196-198	3
α-helix	199-203	5
α-helix	204-224	21
α-helix	228-247	20
α-helix	258-269	12
α-helix	274-285	12
α-helix	290-299	10
α-helix	307-318	12

Chain 8: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	13
β-strand	9	1	14
β-strand	10	1	15
β-strand	12	1	14
β-strand	15	1	13
α-helix	24-26	3
α-helix	27-31	5
α-helix	33-35	3
β-strand	43-44	2	16
α-helix	57-60	4
β-strand	74	1	13
β-strand	77-78	2	16
β-strand	90	1	15
α-helix	91-94	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Core-binding factor subunit beta	0, 5	protein	157	Homo sapiens	Q13951 (AlphaFold model)
Virion infectivity factor	1, 6	protein	178	Human immunodeficiency virus 1	P12504
Elongin-B	3, 8	protein	102	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	4, 9	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Cullin-5	2, 7	protein	314	Homo sapiens	Q93034

Sequence of entity 1 (0, 5), FASTA

>8FVJ_1 Core-binding factor subunit beta (chains 0, 5)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRD

Sequence of entity 2 (1, 6), FASTA

>8FVJ_2 Virion infectivity factor (chains 1, 6)
GPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTHPKISSEVHIP
LGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSES
AIRNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Sequence of entity 3 (3, 8), FASTA

>8FVJ_3 Elongin-B (chains 3, 8)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDV

Sequence of entity 4 (4, 9), FASTA

>8FVJ_4 Elongin-C (chains 4, 9)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 5 (2, 7), FASTA

>8FVJ_5 Cullin-5 (chains 2, 7)
GPAGSSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALK
EDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNK
KSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVN
LCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRAL
RYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNG
IEPMLKDLEEHIIS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H. Ito, F., Alvarez-Cabrera, A.L., Kim, K. et al. Nat Commun (2023) 14:5241-5241. DOI 10.1038/s41467-023-40955-x · PubMed

Other PDB entries of the same protein (UniProt Q13951 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8J62 2.5 Å, Cryo-EM structure of APOBEC3G-Vif complex
1E50 2.6 Å, AML1/CBFbeta complex
1H9D 2.6 Å, Aml1/cbf-beta/dna complex
8CX0 2.7 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex
8H0I 2.8 Å, Cryo-EM structure of APOBEC3G-Vif complex
6P59 2.94 Å, Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex
8CX2 3.2 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2
9ZY0 3.2 Å, Cryo-EM structure of the monomeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
9ZY1 3.2 Å, Cryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
8FVI 3.24 Å, Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
4N9F 3.3 Å, Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex
8CX1 3.3 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1

Browse structure collections

About this viewer

MolViewer shows 8FVJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.