8CX0: DNA dC->dU-editing enzyme APOBEC-3G
Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex. Determined by electron microscopy at 2.7 Å resolution. Released 15 Feb 2023.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organisms
- Homo sapiens, Human immunodeficiency virus 1, Spodoptera frugiperda
- Chains
- 6
- Atoms
- 7,575
- Mol. weight
- 122.55 kDa
- Ligands
- ZN
- Released
- 15 Feb 2023
Explore 8CX0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8CX0 contains 43 α-helices and 40 β-strands across 5 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: 19 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9 | 1 | 1 |
| β-strand | 12 | 1 | 2 |
| α-helix | 14-20 | 7 | |
| β-strand | 32-41 | 10 | 1 |
| β-strand | 50-57 | 8 | 1 |
| α-helix | 62-64 | 3 | |
| α-helix | 66-77 | 12 | |
| α-helix | 78-80 | 3 | |
| β-strand | 86-94 | 9 | 1 |
| α-helix | 98-110 | 13 | |
| β-strand | 114-122 | 9 | 1 |
| α-helix | 129-135 | 7 | |
| α-helix | 136-140 | 5 | |
| β-strand | 147-151 | 5 | 1 |
| α-helix | 154-164 | 11 | |
| β-strand | 165 | 1 | 2 |
| α-helix | 178-193 | 16 | |
| β-strand | 197 | 1 | 3 |
| α-helix | 199-205 | 7 | |
| β-strand | 219-228 | 10 | 4 |
| β-strand | 231-243 | 13 | 4 |
| α-helix | 244-247 | 4 | |
| α-helix | 255-257 | 3 | |
| α-helix | 258-265 | 8 | |
| α-helix | 266-269 | 4 | |
| β-strand | 277-283 | 7 | 4 |
| α-helix | 289-301 | 13 | |
| β-strand | 305-311 | 7 | 4 |
| α-helix | 320-331 | 12 | |
| β-strand | 334-337 | 4 | 4 |
| α-helix | 340-350 | 11 | |
| β-strand | 351 | 1 | 3 |
| α-helix | 356-358 | 3 | |
| α-helix | 364-380 | 17 | |
Chain B: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-13 | 9 | 5 |
| α-helix | 15-30 | 16 | |
| β-strand | 39-41 | 3 | 5 |
| α-helix | 43-45 | 3 | |
| β-strand | 51-59 | 9 | 5 |
| β-strand | 62-69 | 8 | 5 |
| β-strand | 83-91 | 9 | 5 |
| β-strand | 94-97 | 4 | 5 |
| α-helix | 100-107 | 8 | |
| α-helix | 119-124 | 6 | |
| α-helix | 136-138 | 3 | |
| α-helix | 145-153 | 9 | |
| α-helix | 155-157 | 3 | |
| α-helix | 162-164 | 3 | |
| α-helix | 166-169 | 4 | |
Chain C: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| β-strand | 25-29 | 5 | 5 |
| α-helix | 37-50 | 14 | |
| β-strand | 55-59 | 5 | 5 |
| β-strand | 64-70 | 7 | 5 |
| α-helix | 77-79 | 3 | |
| β-strand | 85-87 | 3 | 5 |
| β-strand | 94-103 | 10 | 5 |
| β-strand | 106-115 | 10 | 5 |
| β-strand | 120-127 | 8 | 5 |
| α-helix | 130-134 | 5 | |
| α-helix | 137-148 | 12 | |
Chain D: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 6 |
| β-strand | 12-18 | 7 | 6 |
| β-strand | 23 | 1 | 7 |
| α-helix | 24-35 | 12 | |
| α-helix | 39-41 | 3 | |
| β-strand | 45-46 | 2 | 6 |
| β-strand | 49-50 | 2 | 6 |
| β-strand | 56 | 1 | 7 |
| α-helix | 57-60 | 4 | |
| α-helix | 64-66 | 3 | |
| β-strand | 68 | 1 | 8 |
| β-strand | 71 | 1 | 8 |
| β-strand | 73-76 | 4 | 6 |
| α-helix | 91-94 | 4 | |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 19-22 | 4 | 6 |
| β-strand | 28-31 | 4 | 6 |
| α-helix | 33-37 | 5 | |
| α-helix | 40-45 | 6 | |
| β-strand | 59-61 | 3 | 6 |
| α-helix | 67-83 | 17 | |
| α-helix | 90-92 | 3 | |
| α-helix | 97-110 | 14 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA dC->dU-editing enzyme APOBEC-3G | A | protein | 421 | Homo sapiens | Q9HC16 (AlphaFold model) |
| Virion infectivity factor | B | protein | 192 | Human immunodeficiency virus 1 | P69723 |
| Core-binding factor subunit beta | C | protein | 182 | Homo sapiens | Q13951 (AlphaFold model) |
| Elongin-B | D | protein | 118 | Homo sapiens | Q15370 (AlphaFold model) |
| Elongin-C | E | protein | 112 | Homo sapiens | Q15369 |
| RNA (5'-r(p*ap*ap*ap*ap*ap*ap*ap*a)-3') | K | RNA | 8 | Spodoptera frugiperda | |
Sequence of entity 1 (A), FASTA
>8CX0_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
MKPHFRNTVERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSRPPLDAKIFRGQVYS
ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRDMATFLAEDPKVTLTIFV
ARLYYFWDPDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK
YYILLHIMLGEILRHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVLLNQRRG
FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFIS
KNKHVSLCIFTARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGCPFQP
WDGLDEHSQDLSGRLRAILQNQENGSSLEGGGGWSHPQFEKGGGSGGGSGGGSWSHPQFE
K
Sequence of entity 2 (B), FASTA
>8CX0_2 Virion infectivity factor (chains B)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLG
DARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAI
RKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKT
KGHRGSHTMNGH
Sequence of entity 3 (C), FASTA
>8CX0_3 Core-binding factor subunit beta (chains C)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQLLAVTGKKTT
RP
Sequence of entity 4 (D), FASTA
>8CX0_4 Elongin-B (chains D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 5 (E), FASTA
>8CX0_5 Elongin-C (chains E)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 6 (K), FASTA
>8CX0_6 RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3') (chains K)
AAAAAAAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Li, Y.L., Langley, C.A., Azumaya, C.M. et al. Nature (2023) 615:728-733. DOI 10.1038/s41586-023-05779-1 · PubMed
Other PDB entries of the same protein (UniProt Q9HC16 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3V4K 1.38 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
- 7UXD 1.5 Å, Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy…
- 4ROW 1.7 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
- 4ROV 1.8 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
- 6BUX 1.86 Å, Crystal structure of APOBEC3G catalytic domain complex with substrate ssDNA
- 5ZVB 2.0 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)
- 3V4J 2.04 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
- 3IR2 2.25 Å, Crystal structure of the APOBEC3G catalytic domain
- 3E1U 2.3 Å, The Crystal Structure of the Anti-Viral APOBEC3G Catalytic Domain
- 3IQS 2.3 Å, Crystal structure of the anti-viral APOBEC3G catalytic domain
- 5ZVA 2.3 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
- 8J62 2.5 Å, Cryo-EM structure of APOBEC3G-Vif complex
Browse structure collections
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