SMTL ID : 3nc0.1 (2 other biounits)

Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-1-2-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: T.67 No protein-ligand interaction detected (PLIP) GOL.2: 2 residues within 4Å: Chain A: N.236, E.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236 GOL.3: 1 residues within 4Å: Chain A: K.448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.448 GOL.8: 1 residues within 4Å: Ligands: PEG.5 No protein-ligand interaction detected (PLIP) GOL.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.13: 3 residues within 4Å: Chain C: T.38, L.39, E.42 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:Q.44 Hydrogen bonds: C:L.39, C:E.42 GOL.15: 1 residues within 4Å: Chain D: Q.673 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.673 GOL.22: 1 residues within 4Å: Chain D: E.363 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.363

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 1 residues within 4Å: Chain A: F.388 No protein-ligand interaction detected (PLIP) PEG.5: 2 residues within 4Å: Chain A: E.657 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.657 PEG.6: 3 residues within 4Å: Chain A: K.524, L.527, G.528 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.527, A:Q.532 PEG.7: 2 residues within 4Å: Chain A: M.610 Chain B: T.299 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.618 PEG.14: 2 residues within 4Å: Chain C: E.66, R.72 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:Q.83 Hydrogen bonds: C:E.66, C:R.72 PEG.16: 3 residues within 4Å: Chain D: V.443, R.699, K.702 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.699 PEG.17: 7 residues within 4Å: Chain D: C.36, L.37, Y.38, G.40, A.43 Chain E: V.43, W.60 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.40, D:G.40 PEG.18: 4 residues within 4Å: Chain D: S.762, G.763, S.766, R.767 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.762, D:S.766 PEG.19: 3 residues within 4Å: Chain D: D.438, R.748, R.755 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.748, D:R.755, D:R.755 PEG.20: 4 residues within 4Å: Chain D: K.197, N.236, W.237, P.239 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.236 PEG.21: 3 residues within 4Å: Chain D: K.146, H.147, P.149 No protein-ligand interaction detected (PLIP)

1 x IPH: PHENOL(Non-covalent)

IPH.9: 2 residues within 4Å: Chain A: D.770 Chain B: H.351 No protein-ligand interaction detected (PLIP)

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.11: 25 residues within 4Å: Chain C: D.14, G.15, G.16, T.17, G.18, K.19, T.20, T.21, F.31, E.32, K.33, K.34, Y.35, A.37, T.38, A.63, G.64, N.118, K.119, D.121, I.122, S.146, A.147, K.148 Ligands: MG.12 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.16, C:T.17, C:G.18, C:K.19, C:T.20, C:T.21, C:T.21, C:E.32, C:Y.35, C:T.38, C:G.64, C:N.118, C:K.119, C:K.119, C:A.147, C:K.148 Water bridges: C:T.38, C:L.65 Salt bridges: C:K.19, C:K.19, C:D.121 pi-Stacking: C:F.31, C:F.31 pi-Cation interactions: C:K.119 GTP.23: 26 residues within 4Å: Chain E: D.14, G.15, G.16, T.17, G.18, K.19, T.20, T.21, F.31, E.32, K.33, K.34, Y.35, V.36, A.37, T.38, A.63, G.64, N.118, K.119, D.121, I.122, S.146, A.147, K.148 Ligands: MG.24 22 PLIP interactions: 22 interactions with chain E Hydrogen bonds: E:D.14, E:G.16, E:T.17, E:G.18, E:K.19, E:T.20, E:T.21, E:E.32, E:T.38, E:T.38, E:G.64, E:N.118, E:K.119, E:K.119, E:S.146, E:A.147, E:K.148 Salt bridges: E:K.19, E:K.19, E:D.121 pi-Stacking: E:F.31, E:F.31

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 5 residues within 4Å: Chain C: T.20, T.38, D.61, T.62 Ligands: GTP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.20, C:T.38 MG.24: 6 residues within 4Å: Chain E: K.19, T.20, T.38, D.61, T.62 Ligands: GTP.23 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.20, E:T.38, E:D.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guttler, T. et al., NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-10-27

Peptides

Exportin-1: AD
Snurportin-1: B
GTP-binding nuclear protein Ran: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
F

Exportin-1

Snurportin-1

GTP-binding nuclear protein Ran

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