SMTL ID : 8w9m.1

Cryo-EM structure of the cyanobacterial nitrate transporter NrtBCD in complex with ATP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain C: F.14, Y.22, A.24, H.43, S.44, G.45, C.46, G.47, K.48, S.49, T.50, Q.85, Q.164, H.197 Chain D: K.149, Q.153, I.154, S.155, G.156, G.157, M.158 Ligands: MG.2 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.45, C:G.45, C:C.46, C:G.47, C:K.48, C:S.49, C:T.50, C:T.50, C:Q.85, C:Q.164, D:K.149, D:S.155, D:G.156, D:G.157, D:M.158 Salt bridges: C:K.48, C:K.48, C:H.197 pi-Stacking: C:F.14, C:F.14 ATP.3: 21 residues within 4Å: Chain C: K.134, E.138, S.140, G.141, G.142, M.143 Chain D: Y.30, Y.37, V.39, H.58, S.59, G.60, C.61, G.62, K.63, S.64, T.65, Q.100, Q.179, H.212 Ligands: MG.4 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Y.37, D:S.59, D:S.59, D:G.60, D:G.60, D:C.61, D:G.62, D:K.63, D:S.64, D:T.65, D:Q.100, D:Q.179, C:S.140, C:G.141, C:G.142, C:M.143 Salt bridges: D:K.63, D:K.63, D:H.212 pi-Stacking: D:Y.30, D:Y.30

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain C: S.49, Q.85 Chain D: S.155, G.156 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.49 MG.4: 5 residues within 4Å: Chain C: S.140, G.141 Chain D: S.64, Q.100 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, B. et al., Allosteric regulation of nitrate transporter NRT via the signaling protein PII. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-02-28

Peptides

Nitrate transport permease protein: AB
Nitrate transport ATP-binding protein: C
Nitrate transport ATP-binding protein: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Nitrate transport permease protein

Nitrate transport ATP-binding protein

Nitrate transport ATP-binding protein

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