8E40: Full-length APOBEC3G

Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA. Determined by electron microscopy at 3.57 Å resolution. Released 11 Jan 2023.

Method
Electron microscopy
Resolution
3.57 Å
Organisms
Macaca mulatta, Human immunodeficiency virus 1, Homo sapiens
Chains
5
Atoms
6,297
Mol. weight
99.97 kDa
Ligands
ZN
Released
11 Jan 2023

Explore 8E40 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E40 contains 30 α-helices and 29 β-strands across 3 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: 20 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix17-204
β-strand32-3651
β-strand3812
α-helix47-482
β-strand53-5751
α-helix66-7813
β-strand86-8723
β-strand8912
β-strand90-9231
α-helix95-973
α-helix98-11013
β-strand114-11523
β-strand118-12031
α-helix129-14113
β-strand150-15121
α-helix154-16411
α-helix170-1723
α-helix174-1752
α-helix179-19214
β-strand19714
α-helix199-2013
α-helix202-2065
β-strand222-22545
β-strand234-24075
α-helix243-2464
α-helix260-2656
α-helix267-2693
β-strand276-28275
α-helix291-30010
β-strand304-31075
α-helix320-33011
β-strand334-33635
α-helix339-34810
β-strand35014
α-helix355-3573
α-helix363-37816
Chain B: 4 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand6-1386
α-helix15-2612
α-helix27-315
β-strand39-4136
β-strand51-5996
β-strand62-6986
β-strand83-9086
β-strand9716
α-helix100-1089
α-helix167-1704
Chain C: 6 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix6-127
α-helix16-216
β-strand25-2956
α-helix37-4913
β-strand55-5846
β-strand64-6966
α-helix71-744
β-strand85-8736
β-strand95-10396
β-strand106-11496
β-strand120-12786
α-helix131-1344
α-helix140-1489

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA dC->dU-editing enzyme APOBEC-3GAprotein386Macaca mulattaQ7YR23 (AlphaFold model)
Virion infectivity factorBprotein178Human immunodeficiency virus 1P12504
Core-binding factor subunit betaCprotein157Homo sapiensQ13951 (AlphaFold model)
RNARRNA22Escherichia coli
RNArRNA25Escherichia coli
Sequence of entity 1 (A), FASTA
>8E40_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
GPGGSGGMKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKI
FQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPK
VTLTIFVARLYYFWDPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNN
LPKHYTLLQATLGELLRHLMDPGTFTSNFNNKPWVSGQHETYLCYKVERLHNDTWVPLNQ
HRGFLRNQAPNIHGFPKGRHAQLCFLDLIPFWKLDGQQYRVTCFTSWSPCFSCAQEMAKF
ISNNEHVSLCIFAARIYDDQGRYQEGLRTLHRDGAKIAMMNYSEFEYCWDTFVDRQGRPF
QPWDGLDEHSQALSGRLRAILQNQGN
Sequence of entity 2 (B), FASTA
>8E40_2 Virion infectivity factor (chains B)
GPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIP
LGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSES
AIRNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK
Sequence of entity 3 (C), FASTA
>8E40_3 Core-binding factor subunit beta (chains C)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRD
Sequence of entity 4 (R), FASTA
>8E40_4 RNA (chains R)
UUUUUUUUUUUUUUAAAAAAAA
Sequence of entity 5 (r), FASTA
>8E40_5 RNA (chains r)
UUUUUUUUAAAAAAAAAAAAAAAAA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2

Primary citation

Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase. Ito, F., Alvarez-Cabrera, A.L., Liu, S. et al. Sci Adv (2023) 9:eade3168-eade3168. DOI 10.1126/sciadv.ade3168 · PubMed

Other PDB entries of the same protein (UniProt Q7YR23 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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