SMTL ID : 8wm7.1

Cryo-EM structure of cyanobacterial nitrate/nitrite transporter NrtBCD in complex with signalling protein PII

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-3-mer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain C: F.14, D.15, L.16, Y.22, A.24, S.44, G.45, C.46, G.47, K.48, S.49, T.50 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.22, C:G.45, C:K.48, C:S.49, C:S.49, C:T.50, C:T.50 Salt bridges: C:K.48 pi-Stacking: C:F.14, C:F.14 ADP.2: 12 residues within 4Å: Chain D: Y.30, P.31, T.32, Y.37, V.39, S.59, G.60, C.61, G.62, K.63, S.64, T.65 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.37, D:G.60, D:G.62, D:K.63, D:S.64, D:T.65, D:T.65 Salt bridges: D:K.63 pi-Stacking: D:Y.30, D:Y.30 ADP.3: 23 residues within 4Å: Chain E: I.7, G.35, F.36, G.37, R.38, Q.39, K.58, I.86, G.87, D.88, G.89, K.90, F.92 Chain F: V.26, G.27, M.28, T.29, E.62, I.63, V.64, V.65, R.101, R.103 15 PLIP interactions: 6 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:M.28, F:V.64, F:V.64, F:R.101, E:F.36, E:R.38, E:G.87, E:D.88, E:G.89 Salt bridges: F:R.101, F:R.103, E:R.38, E:R.38, E:K.90, E:K.90 ADP.4: 24 residues within 4Å: Chain E: I.25, G.27, M.28, T.29, E.62, I.63, V.64, R.101, R.103, V.112 Chain G: I.7, G.35, F.36, G.37, R.38, Q.39, L.56, K.58, I.86, G.87, D.88, G.89, K.90, F.92 15 PLIP interactions: 10 interactions with chain G, 5 interactions with chain E Hydrogen bonds: G:F.36, G:G.37, G:Q.39, G:K.58, G:G.87, G:G.87, G:D.88, G:G.89, G:G.89, G:K.90, E:M.28, E:V.64, E:V.64 Salt bridges: E:R.101, E:R.103 ADP.5: 23 residues within 4Å: Chain F: I.7, G.35, F.36, G.37, R.38, L.56, K.58, I.86, G.87, D.88, G.89, K.90, F.92 Chain G: I.25, G.27, M.28, T.29, E.62, I.63, V.64, V.65, R.101, R.103 17 PLIP interactions: 11 interactions with chain F, 6 interactions with chain G Hydrogen bonds: F:R.38, F:K.58, F:G.87, F:D.88, F:G.89, F:K.90, G:V.64, G:V.64, G:R.103 Salt bridges: F:R.38, F:R.38, F:K.90, F:K.90, G:R.101, G:R.101, G:R.103 pi-Cation interactions: F:K.90

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
Nitrogen regulatory protein P-II: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

F
F

G
G

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

Nitrogen regulatory protein P-II

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