SMTL ID : 8fvi.1

Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x A- A- A- A- A- A- A- A- A: RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

A-A-A-A-A-A-A-A-A.1: 19 residues within 4Å: Chain C: R.25, R.27, R.28, H.121, W.122, Q.127, K.175, A.179, R.182, R.183, R.186 Chain D: U.3, U.4, U.5, U.6, U.7, U.8, U.9, U.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.31, C:R.33, C:L.118, C:Y.120 pi-Stacking: C:Y.30, C:W.89, C:W.122

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: H.110, C.116, C.135, H.141 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.110, B:C.116, B:C.135, B:H.141 ZN.3: 3 residues within 4Å: Chain C: H.61, C.92, C.95 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.61, C:C.92, C:C.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, F. et al., Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H. Nat Commun (2023)

Release Date

2023-09-06

Peptides

Core-binding factor subunit beta: A
Virion infectivity factor: B
DNA dC->dU-editing enzyme APOBEC-3H: C
Cullin 5: E
Elongin-B: F
Elongin-C: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

C
A

E
x

F
y

G
z

Core-binding factor subunit beta

Virion infectivity factor

DNA dC->dU-editing enzyme APOBEC-3H

Cullin 5

Elongin-B

Elongin-C

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