4N9F: Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex

Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex. Determined by X-ray diffraction at 3.3 Å resolution. Released 8 Jan 2014.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 60
Atoms: 77,274
Mol. weight: 1200.46 kDa
Ligands: ZN
Released: 8 Jan 2014

Explore 4N9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N9F contains 491 α-helices and 355 β-strands across 60 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	16-20	5
β-strand	25-29	5	69
α-helix	37-49	13
β-strand	55-58	4	69
β-strand	64-70	7	69
β-strand	85-87	3	69
β-strand	94-99	6	69
β-strand	102-103	2	69
β-strand	106-115	10	69
β-strand	120-127	8	69
α-helix	129-134	6
α-helix	137-148	12
β-strand	155	1	70

Chain 1: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	69
α-helix	15-30	16
β-strand	39-41	3	69
β-strand	51-59	9	69
β-strand	62-69	8	69
β-strand	83-91	9	69
β-strand	94-97	4	69
α-helix	100-110	11
β-strand	116	1	70
α-helix	118-125	8
α-helix	136-138	3
α-helix	146-154	9
α-helix	163-165	3
α-helix	167-170	4

Chain 2: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	32
β-strand	11-13	3	33
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	33
β-strand	51-59	9	33
β-strand	62-69	8	33
β-strand	83-91	9	33
β-strand	94-97	4	33
α-helix	100-110	11
β-strand	116	1	34
α-helix	117-125	9
α-helix	146-154	9
α-helix	163-165	3
α-helix	167-170	4

Chain 3: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	16-31	16
α-helix	37-53	17
α-helix	57-81	25
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	196-197	2
α-helix	198-203	6
α-helix	204-225	22
α-helix	227-248	22
α-helix	257-269	13
α-helix	271-273	3
α-helix	274-278	5
α-helix	281-287	7
α-helix	290-300	11
α-helix	307-318	12

Chain 4: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	73
β-strand	10	1	75
β-strand	12-19	8	73
β-strand	23	1	76
α-helix	24-35	12
β-strand	43-44	2	77
β-strand	45-46	2	78
β-strand	49-50	2	78
β-strand	56	1	76
α-helix	58-60	3
β-strand	68	1	79
β-strand	71	1	79
α-helix	72	1
β-strand	73-74	2	73
β-strand	77-78	2	77
β-strand	90	1	75
α-helix	91-97	7

Chain 5: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	73
β-strand	28-32	5	73
α-helix	33-37	5
α-helix	40-46	7
β-strand	59-61	3	73
α-helix	67-83	17
α-helix	97-110	14

Chain 6: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
α-helix	16-21	6
β-strand	25-30	6	83
α-helix	37-49	13
β-strand	55-58	4	83
β-strand	64-70	7	83
β-strand	85-87	3	83
β-strand	94-99	6	83
β-strand	102-103	2	83
β-strand	106-115	10	83
β-strand	120-127	8	83
α-helix	129-134	6
α-helix	137-148	12

Chain 7: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	83
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	83
β-strand	54-59	6	83
β-strand	62-68	7	83
β-strand	83-91	9	83
β-strand	94-97	4	83
α-helix	100-110	11
α-helix	117-125	9
α-helix	136-138	3
α-helix	145-153	9
α-helix	162-164	3
α-helix	166-169	4

49 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-5	3, 9, C, I, O, U, V, f, l, r, w, x	protein	311	Homo sapiens	Q93034 (AlphaFold model)
Transcription elongation factor B polypeptide 1	5, B, E, K, Q, T, Y, Z, h, n, t, z	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Transcription elongation factor B polypeptide 2	4, D, H, J, P, W, X, e, g, m, s, y	protein	102	Homo sapiens	Q15370 (AlphaFold model)
Core-binding factor subunit beta	0, 6, F, L, N, R, a, c, i, k, o, u	protein	170	Homo sapiens	Q13951 (AlphaFold model)
Virion infectivity factor	1, 2, 7, G, M, S, b, d, j, p, q, v	protein	176	Human immunodeficiency virus 1	P12504

Sequence of entity 1 (3, 9, C, I, O, U, V, f, l, r, w, x), FASTA

>4N9F_1 Cullin-5 (chains 3, 9, C, I, O, U, V, f, l, r, w, x)
ASLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDIL
EFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNV
EDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCSN
PEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLE
TRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPM
LKDLEEHIISA

Sequence of entity 2 (5, B, E, K, Q, T, Y, Z, h, n, t, z), FASTA

>4N9F_2 Transcription elongation factor B polypeptide 1 (chains 5, B, E, K, Q, T, Y, Z, h, n, t, z)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (4, D, H, J, P, W, X, e, g, m, s, y), FASTA

>4N9F_3 Transcription elongation factor B polypeptide 2 (chains 4, D, H, J, P, W, X, e, g, m, s, y)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDV

Sequence of entity 4 (0, 6, F, L, N, R, a, c, i, k, o, u), FASTA

>4N9F_4 Core-binding factor subunit beta (chains 0, 6, F, L, N, R, a, c, i, k, o, u)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQ

Sequence of entity 5 (1, 2, 7, G, M, S, b, d, j, p, q, v), FASTA

>4N9F_5 Virion infectivity factor (chains 1, 2, 7, G, M, S, b, d, j, p, q, v)
MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLG
DAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAI
RNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

Primary citation

Structural basis for hijacking CBF-b and CUL5 E3 ligase complex by HIV-1 Vif. Guo, Y.Y., Dong, L.Y., Qiu, X.L. et al. Nature (2014) 505:229-233.

Other PDB entries of the same protein (UniProt Q93034 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DPL 2.6 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
8EI2 2.8 Å, Crystal structure of the N-terminal domain of CUL5 in complex with H314, a Helicon…
9T7V 2.95 Å, Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
9SDX 2.97 Å, Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub
3DQV 3.0 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
4JGH 3.0 Å, Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5
9SDY 3.06 Å, Structure of RBR E2 variant binding to CUL5-RBX2 bound ARIH2
8FVI 3.24 Å, Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
7ONI 3.4 Å, Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2*
9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
8FVJ 3.54 Å, Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5
9OMA 4.14 Å, Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)

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