8FVI: Human APOBEC3H
Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5. Determined by electron microscopy at 3.24 Å resolution. Released 6 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.24 Å
- Organisms
- Homo sapiens, Human immunodeficiency virus 1, Escherichia coli
- Chains
- 8
- Atoms
- 6,774
- Mol. weight
- 126.94 kDa
- Ligands
- ZN
- Released
- 6 Sept 2023
Explore 8FVI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8FVI contains 42 α-helices and 27 β-strands across 6 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: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-14 | 7 | |
| α-helix | 16-21 | 6 | |
| β-strand | 25-30 | 6 | 1 |
| α-helix | 37-49 | 13 | |
| β-strand | 55-57 | 3 | 1 |
| β-strand | 64-70 | 7 | 1 |
| α-helix | 71-73 | 3 | |
| β-strand | 99-103 | 5 | 1 |
| β-strand | 106-113 | 8 | 1 |
| β-strand | 120-127 | 8 | 1 |
| α-helix | 129-134 | 6 | |
| α-helix | 138-148 | 11 | |
Chain 1: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-11 | 7 | 1 |
| α-helix | 15-26 | 12 | |
| α-helix | 27-31 | 5 | |
| β-strand | 41 | 1 | 1 |
| β-strand | 51-59 | 9 | 1 |
| β-strand | 62-69 | 8 | 1 |
| β-strand | 84-91 | 8 | 1 |
| β-strand | 94-97 | 4 | 1 |
| α-helix | 100-108 | 9 | |
| α-helix | 117-119 | 3 | |
| α-helix | 120-125 | 6 | |
| α-helix | 136-138 | 3 | |
| α-helix | 146-154 | 9 | |
| α-helix | 167-170 | 4 | |
Chain A: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 2 |
| α-helix | 6-12 | 7 | |
| α-helix | 24-26 | 3 | |
| β-strand | 29-36 | 8 | 3 |
| α-helix | 40-42 | 3 | |
| β-strand | 43-48 | 6 | 3 |
| α-helix | 55-66 | 12 | |
| β-strand | 74-80 | 7 | 3 |
| α-helix | 86-98 | 13 | |
| β-strand | 102-108 | 7 | 3 |
| α-helix | 117-128 | 12 | |
| β-strand | 133-135 | 3 | 3 |
| α-helix | 138-147 | 10 | |
| β-strand | 149 | 1 | 2 |
| α-helix | 159-169 | 11 | |
| α-helix | 172-180 | 9 | |
Chain x: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-29 | 11 | |
| α-helix | 30-32 | 3 | |
| α-helix | 37-53 | 17 | |
| α-helix | 57-81 | 25 | |
| α-helix | 86-106 | 21 | |
| α-helix | 112-117 | 6 | |
| α-helix | 135-143 | 9 | |
| α-helix | 144-148 | 5 | |
Chain y: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 4 |
| β-strand | 10 | 1 | 5 |
| β-strand | 12-18 | 7 | 4 |
| α-helix | 24-27 | 4 | |
| α-helix | 32-35 | 4 | |
| α-helix | 57-60 | 4 | |
| α-helix | 64-66 | 3 | |
| α-helix | 72 | 1 | |
| β-strand | 73-74 | 2 | 4 |
| β-strand | 90 | 1 | 5 |
| α-helix | 92-94 | 3 | |
Chain z: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 19-22 | 4 | 6 |
| β-strand | 28-31 | 4 | 6 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 60-61 | 2 | 6 |
| α-helix | 67-83 | 17 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-110 | 14 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Core-binding factor subunit beta | 0 | protein | 157 | Homo sapiens | Q13951 (AlphaFold model) |
| Virion infectivity factor | 1 | protein | 178 | Human immunodeficiency virus 1 | P12504 |
| DNA dC->dU-editing enzyme APOBEC-3H | A | protein | 189 | Homo sapiens | Q6NTF7 (AlphaFold model) |
| RNA(5'-r(ap*up*up*up*up*up*up*up*up*u)-3') | B | RNA | 10 | Escherichia coli | |
| RNA(5'-r(*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') | C | RNA | 9 | Escherichia coli | |
| Cullin 5 | x | protein | 314 | Homo sapiens | Q93034 (AlphaFold model) |
| Elongin-B | y | protein | 102 | Homo sapiens | Q15370 |
| Elongin-C | z | protein | 96 | Homo sapiens | Q15369 |
Sequence of entity 1 (0), FASTA
>8FVI_1 Core-binding factor subunit beta (chains 0)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRD
Sequence of entity 2 (1), FASTA
>8FVI_2 Virion infectivity factor (chains 1)
GPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTHPKISSEVHIP
LGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSES
AIRNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK
Sequence of entity 3 (A), FASTA
>8FVI_3 DNA dC->dU-editing enzyme APOBEC-3H (chains A)
GPGGSGGMALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKC
HAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIQAHDHLNLRIFASRLYY
HWCKPQQDGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPLSFNPYKMLEELDKNSRAI
KRRLDRIKS
Sequence of entity 4 (B), FASTA
>8FVI_4 RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') (chains B)
AUUUUUUUUU
Sequence of entity 5 (C), FASTA
>8FVI_5 RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') (chains C)
AAAAAAAAA
Sequence of entity 6 (x), FASTA
>8FVI_6 Cullin 5 (chains x)
GPAGSSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALK
EDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNK
KSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVN
LCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRAL
RYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNG
IEPMLKDLEEHIIS
Sequence of entity 7 (y), FASTA
>8FVI_7 Elongin-B (chains y)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDV
Sequence of entity 8 (z), FASTA
>8FVI_8 Elongin-C (chains z)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H. Ito, F., Alvarez-Cabrera, A.L., Kim, K. et al. Nat Commun (2023) 14:5241-5241. DOI 10.1038/s41467-023-40955-x · PubMed
Other PDB entries of the same protein (UniProt Q13951 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8J62 2.5 Å, Cryo-EM structure of APOBEC3G-Vif complex
- 1E50 2.6 Å, AML1/CBFbeta complex
- 1H9D 2.6 Å, Aml1/cbf-beta/dna complex
- 8CX0 2.7 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex
- 8H0I 2.8 Å, Cryo-EM structure of APOBEC3G-Vif complex
- 6P59 2.94 Å, Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex
- 8CX2 3.2 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2
- 9ZY0 3.2 Å, Cryo-EM structure of the monomeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
- 9ZY1 3.2 Å, Cryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
- 4N9F 3.3 Å, Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex
- 8CX1 3.3 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1
- 8FVJ 3.54 Å, Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5
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