SMTL ID : 8cx2.1

Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

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

A-A-U-A-A-A-A-A-U.1: 36 residues within 4Å: Chain A: R.24, P.25, I.26, L.27, S.28, R.29, N.31, Q.57, Y.59, W.94, L.123, Y.124, Y.125, F.126, W.127, F.268, K.270 Chain B: R.19, T.20, K.22, S.23, K.26, H.27, Y.30, V.31, Y.40, H.42, H.43, Y.44 Chain F: R.6, V.9, R.11, M.12, Y.13, T.16, W.34 Protein-ligand interaction information (PLIP) not available

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

U-U-U-A-A-A-A-A-U.2: 37 residues within 4Å: Chain A: R.6, V.9, R.11, M.12, Y.13, T.16, W.34, R.55 Chain F: R.24, P.25, I.26, L.27, S.28, R.29, N.31, Q.57, Y.59, W.94, L.123, Y.124, Y.125, F.126, W.127, F.268, K.270 Chain G: R.19, T.20, K.22, S.23, K.26, H.27, Y.30, V.31, Y.40, H.42, H.43, Y.44 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.257, C.288, C.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.257, A:C.288, A:C.291 ZN.4: 4 residues within 4Å: Chain A: H.65, E.67, C.97, C.100 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:C.97, A:C.100 ZN.5: 4 residues within 4Å: Chain B: H.108, C.114, C.133, H.139 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.108, B:C.114, B:C.133, B:H.139 ZN.6: 3 residues within 4Å: Chain F: H.257, C.288, C.291 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.257, F:C.288, F:C.291 ZN.7: 4 residues within 4Å: Chain F: H.65, E.67, C.97, C.100 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.65, F:E.67, F:C.97, F:C.100 ZN.8: 5 residues within 4Å: Chain G: H.108, C.114, C.133, Y.135, H.139 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.108, G:C.114, G:C.133, G:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y.L. et al., The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Nature (2023)

Release Date

2023-02-15

Peptides

DNA dC->dU-editing enzyme APOBEC-3G: AF
Virion infectivity factor: BG
Core-binding factor subunit beta: CH
Elongin-B: DI
Elongin-C: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

B
B

G
G

C
C

H
H

D
D

I
I

E
E

J
J

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

Virion infectivity factor

Core-binding factor subunit beta

Elongin-B

Elongin-C

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