6P59: SIVrcm Vif-CBFbeta-ELOB-ELOC complex

Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex. Determined by X-ray diffraction at 2.94 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.94 Å
Organisms: Homo sapiens, Simian immunodeficiency virus
Chains: 8
Atoms: 8,925
Mol. weight: 142.43 kDa
Ligands: ZN
Released: 25 Dec 2019

Explore 6P59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P59 contains 58 α-helices and 62 β-strands across 8 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 A: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
β-strand	25-28	4	7
α-helix	37-49	13
β-strand	55-59	5	7
β-strand	64-70	7	7
α-helix	71-73	3
β-strand	82	1	7
β-strand	86-87	2	7
β-strand	94-103	10	7
β-strand	106-115	10	7
β-strand	120-127	8	7
α-helix	129-133	5
α-helix	139-148	10
β-strand	155	1	8

Chain B: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	7
α-helix	16-31	16
β-strand	41-43	3	7
α-helix	45-47	3
β-strand	54-61	8	7
β-strand	66-76	11	7
β-strand	85-94	10	7
β-strand	101-104	4	7
α-helix	107-114	8
β-strand	123	1	8
α-helix	126-132	7
β-strand	136	1	13
α-helix	142-144	3
α-helix	149-151	3
α-helix	152-164	13
β-strand	201	1	13
α-helix	202-205	4
α-helix	208-210	3
α-helix	212-216	5

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
β-strand	24-28	5	1
α-helix	37-49	13
β-strand	55-59	5	1
β-strand	64-70	7	1
α-helix	71-73	3
β-strand	82	1	1
β-strand	86-87	2	1
β-strand	94-103	10	1
β-strand	106-115	10	1
β-strand	120-127	8	1
α-helix	129-134	6
α-helix	136-138	3
α-helix	140-148	9
β-strand	155	1	2
α-helix	156-157	2

Chain D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	9
β-strand	10	1	10
β-strand	12-19	8	9
β-strand	23	1	11
α-helix	24-35	12
α-helix	39-41	3
β-strand	43-46	4	9
β-strand	49-50	2	9
β-strand	56	1	11
α-helix	57-60	4
α-helix	72	1
β-strand	73-78	6	9
β-strand	80-81	2	12
β-strand	84-85	2	12
α-helix	86-88	3
β-strand	90	1	10
α-helix	94-96	3

Chain E: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	9
β-strand	28-32	5	9
α-helix	33-36	4
α-helix	40-46	7
α-helix	54-56	3
β-strand	59-61	3	9
α-helix	67-82	16
α-helix	89-92	4
α-helix	97-109	13

Chain F: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	1
α-helix	16-27	12
α-helix	28-32	5
β-strand	41-43	3	1
α-helix	50	1
β-strand	54-62	9	1
β-strand	66-76	11	1
α-helix	83-84	2
β-strand	85-94	10	1
α-helix	100	1
β-strand	101-104	4	1
α-helix	107-115	9
β-strand	123	1	2
α-helix	126-132	7
α-helix	142-144	3
α-helix	149-151	3
α-helix	152-166	15
α-helix	202-205	4
α-helix	208-210	3
α-helix	212-216	5

Chain W: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	10	1	4
β-strand	12-19	8	3
β-strand	23	1	5
α-helix	24-35	12
α-helix	39-41	3
β-strand	44-46	3	3
β-strand	49-50	2	3
β-strand	56	1	5
α-helix	57-60	4
α-helix	72	1
β-strand	73-77	5	3
α-helix	80	1
β-strand	81	1	6
β-strand	84	1	6
β-strand	90	1	4
α-helix	94-96	3

Chain Z: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	3
α-helix	67-82	16
α-helix	89-92	4
α-helix	97-110	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Core-binding factor subunit beta	A, C	protein	165	Homo sapiens	Q13951 (AlphaFold model)
Elongin-B	D, W	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	E, Z	protein	112	Homo sapiens	Q15369 (AlphaFold model)
Virion infectivity factor	B, F	protein	220	Simian immunodeficiency virus	E1ANT9

Sequence of entity 1 (A, C), FASTA

>6P59_1 Core-binding factor subunit beta (chains A, C)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEME

Sequence of entity 2 (D, W), FASTA

>6P59_2 Elongin-B (chains D, W)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (E, Z), FASTA

>6P59_3 Elongin-C (chains E, Z)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (B, F), FASTA

>6P59_4 Virion infectivity factor (chains B, F)
MAEKMWIVRPVWRVDRRKIEQWHSLVKYHMYKGKKEAREWEYVPHFKVPWGWWSHSEVHI
PLGNNTKIKVTTYWNLTTEKGWLGTYGAALAYIDQKCDPPYFTDIDPIVADSLIHKIYFP
CFTDKAIRQAILGEKVLLCGFQRGHRDQVGTLQYLAIQAWAREQVKKHGRKSARGPHWGW
RSRVPALVGQNAVRNKSGSQVTLPSRVHFPSLAYLCGTLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (MES, GOL) are not listed.

Primary citation

Structural Basis for a Species-Specific Determinant of an SIV Vif Protein toward Hominid APOBEC3G Antagonism. Binning, J.M., Chesarino, N.M., Emerman, M. et al. Cell Host Microbe (2019) 26:739-747.e4. DOI 10.1016/j.chom.2019.10.014 · 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
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
8FVJ 3.54 Å, Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5

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