8J62: APOBEC3G-Vif complex
Cryo-EM structure of APOBEC3G-Vif complex. Determined by electron microscopy at 2.5 Å resolution. Released 19 Jul 2023.
- Method
- Electron microscopy
- Resolution
- 2.5 Å
- Organisms
- Homo sapiens, Human immunodeficiency virus 1, synthetic construct
- Chains
- 12
- Atoms
- 10,448
- Mol. weight
- 247.42 kDa
- Ligands
- ZN
- Released
- 19 Jul 2023
Explore 8J62 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8J62 contains 44 α-helices and 62 β-strands across 10 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 and B: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-9 | 7 | |
| β-strand | 24-32 | 9 | 1 |
| β-strand | 35-38 | 4 | 1 |
| β-strand | 44-46 | 3 | 1 |
| α-helix | 54-65 | 12 | |
| β-strand | 73-81 | 9 | 1 |
| α-helix | 85-97 | 13 | |
| β-strand | 101-109 | 9 | 1 |
| α-helix | 116-127 | 12 | |
| β-strand | 131-134 | 4 | 1 |
| α-helix | 137-146 | 10 | |
| α-helix | 153-155 | 3 | |
| α-helix | 157-158 | 2 | |
| α-helix | 161-176 | 16 | |
Chains C and G: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-12 | 8 | 2 |
| α-helix | 15-30 | 16 | |
| β-strand | 39-41 | 3 | 2 |
| α-helix | 43-45 | 3 | |
| β-strand | 53-59 | 7 | 2 |
| β-strand | 62-69 | 8 | 2 |
| β-strand | 84-91 | 8 | 2 |
| β-strand | 94-97 | 4 | 2 |
| α-helix | 100-110 | 11 | |
| α-helix | 161-164 | 4 | |
| α-helix | 166-170 | 5 | |
Chains D and H: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-23 | 6 | |
| β-strand | 26-29 | 4 | 2 |
| α-helix | 37-49 | 13 | |
| β-strand | 55-59 | 5 | 2 |
| β-strand | 64-70 | 7 | 2 |
| α-helix | 71-73 | 3 | |
| β-strand | 85-87 | 3 | 2 |
| β-strand | 94-103 | 10 | 2 |
| β-strand | 106-115 | 10 | 2 |
| β-strand | 120-127 | 8 | 2 |
Chains E and I: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-13 | 5 | 3 |
| α-helix | 15-30 | 16 | |
| β-strand | 39-41 | 3 | 3 |
| α-helix | 43-45 | 3 | |
| β-strand | 51-59 | 9 | 3 |
| β-strand | 62-72 | 11 | 3 |
| β-strand | 82-91 | 10 | 3 |
| β-strand | 94-97 | 4 | 3 |
| α-helix | 100-110 | 11 | |
| α-helix | 166-170 | 5 | |
Chains F and J: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-29 | 2 | 3 |
| α-helix | 38-50 | 13 | |
| β-strand | 55-58 | 4 | 3 |
| β-strand | 64-68 | 5 | 3 |
| α-helix | 71-73 | 3 | |
| β-strand | 96-103 | 8 | 3 |
| β-strand | 106-114 | 9 | 3 |
| β-strand | 121-126 | 6 | 3 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| APOBEC3G | A, B | protein | 371 | Homo sapiens | Q9HC16 (AlphaFold model) |
| Viral infectivity factor | C, E, G, I | protein | 150 | Human immunodeficiency virus 1 | P12504 |
| Core binding factor beta | D, F, H, J | protein | 156 | Homo sapiens | Q13951 (AlphaFold model) |
| RNA (5'-r(*cp*gp*gp*up*up*gp*ap*up*up*gp*up*up*up*up*ap*ap*cp*ap*a)-3') | X, Y | RNA | 20 | synthetic construct | |
Sequence of entity 1 (A, B), FASTA
>8J62_1 APOBEC3G (chains A, B)
GPGHMDPDTFSYNFNNRPILSRRNTVWLCYEVERLDNGTWVKMDQHRGQVYSELKYHPEM
RFLSLVSKWKLHRDQEYEVTWYISWSPCTKCARDMATFLQENTHVTLTIFVARLYYFWDP
DYQEALRSLAQAGATIKIMNYDEFQHCWSKFVYSQGAPFQPWDGLDEYSQALSGMLGEIL
RHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLNQRRGFLANQAPHKHGFL
EGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIKTAR
IYDDQGRAQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLDEHSQDLSG
RLRAILQNQEN
Sequence of entity 2 (C, E, G, I), FASTA
>8J62_2 Viral infectivity factor (chains C, E, G, I)
MGHHHHHHSQDPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTN
PKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIH
LHYFDEASEGSQIKPPLPSVRKLTEDRWNK
Sequence of entity 3 (D, F, H, J), FASTA
>8J62_3 Core binding factor beta (chains D, F, H, J)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDR
Sequence of entity 4 (X, Y), FASTA
>8J62_4 RNA (5'-R(*CP*GP*GP*UP*UP*GP*AP*UP*UP*GP*UP*UP*UP*UP*AP*AP*CP*AP*A)-3') (chains X, Y)
CGGUUGAUUGUUUUAACAAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural insights into RNA bridging between HIV-1 Vif and antiviral factor APOBEC3G. Kouno, T., Shibata, S., Shigematsu, M. et al. Nat Commun (2023) 14:4037-4037. DOI 10.1038/s41467-023-39796-5 · 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)
- 8CX0 2.7 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex
Browse structure collections
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