6NIL: Truncated HIV-1 Vif/CBFbeta/A3F complex

cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex. Determined by electron microscopy at 3.9 Å resolution. Released 11 Dec 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 12
Atoms: 15,220
Mol. weight: 236.34 kDa
Ligands: ZN
Released: 11 Dec 2019

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

Secondary structure: helices and β-sheets

6NIL contains 72 α-helices and 120 β-strands across 12 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.

Chains A, D, G and J: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	192	1	1
β-strand	195	1	2
α-helix	197-203	7
β-strand	218-222	5	1
β-strand	223-226	4	3
β-strand	234-238	5	1
α-helix	250-257	8
α-helix	258-262	5
β-strand	267-270	4	3
β-strand	273	1	4
β-strand	275	1	1
α-helix	278-280	3
α-helix	284-293	10
β-strand	297	1	3
β-strand	301	1	4
β-strand	302-303	2	5
α-helix	312-320	9
α-helix	322-324	3
β-strand	329-330	2	5
α-helix	333-343	11
β-strand	344	1	2
α-helix	357-369	13

Chains B, E, H and K: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	16-21	6
β-strand	26-28	3	6
α-helix	40-49	10
β-strand	56-58	3	6
β-strand	64-70	7	6
β-strand	85-91	7	6
β-strand	94-103	10	6
β-strand	106-115	10	6
β-strand	121-127	7	6
α-helix	131-133	3
α-helix	141-143	3

Chains C, F, I and L: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	6
α-helix	18-24	7
α-helix	27-31	5
β-strand	39	1	6
β-strand	51	1	7
β-strand	55-59	5	6
β-strand	62-68	7	6
β-strand	69	1	7
β-strand	74	1	8
β-strand	81	1	8
β-strand	83-90	8	6
β-strand	95-97	3	6
α-helix	100-107	8
α-helix	166-169	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3F	A, D, G, J	protein	207	Homo sapiens	Q8IUX4 (AlphaFold model)
Core-binding factor subunit beta	B, E, H, K	protein	151	Homo sapiens	Q13951 (AlphaFold model)
Virion infectivity factor	C, F, I, L	protein	138	Human immunodeficiency virus 1	P12504

Sequence of entity 1 (A, D, G, J), FASTA

>6NIL_1 DNA dC->dU-editing enzyme APOBEC-3F (chains A, D, G, J)
MGSSHHHHHHSQDPNSMGKEILRNPMEAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVK
HHSPVSWKRGVFRNQVDPETGRHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGE
VAEFLARHSNVNLTIKTARLYYFKDTDAAEGLRSLSQEGASVEIMGYKDFKYCWENFVYN
DDEPFKPWDGLDYNFLDLDSKLQEILE

Sequence of entity 2 (B, E, H, K), FASTA

>6NIL_2 Core-binding factor subunit beta (chains B, E, H, K)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTR

Sequence of entity 3 (C, F, I, L), FASTA

>6NIL_3 Virion infectivity factor (chains C, F, I, L)
MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLG
DAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDEASEGSQ
IKPPLPSVRKLTEDRWNK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural basis of antagonism of human APOBEC3F by HIV-1 Vif. Hu, Y., Desimmie, B.A., Nguyen, H.C. et al. Nat Struct Mol Biol (2019) 26:1176-1183. DOI 10.1038/s41594-019-0343-6 · PubMed

Other PDB entries of the same protein (UniProt Q8IUX4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HX4 1.92 Å, Zinc-Free APOBEC3F Catalytic Domain Crystal Structure
5ZVB 2.0 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)
5ZVA 2.3 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
5HX5 2.33 Å, APOBEC3F Catalytic Domain Crystal Structure
3WUS 2.54 Å, Crystal Structure of the Vif-Binding Domain of Human APOBEC3F
8VUD 2.6 Å, Crystal structure of APOBEC3F-CD1
4IOU 2.75 Å, Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F
4J4J 3.1 Å, Crystal structure of the APOBEC3F Vif binding domain
5W2M 3.7 Å, APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA

Browse structure collections

About this viewer

MolViewer shows 6NIL 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.