SMTL ID : 8xuv.1

Cryo-EM structure of tomato NRC2 filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 10 residues within 4Å: Chain A: T.467, K.473, S.669, K.689, N.719, K.721, K.747, T.749, K.773, K.775 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.719, A:T.749 Salt bridges: A:K.473, A:K.473, A:K.689, A:K.689, A:K.721, A:K.721, A:K.721, A:K.721, A:K.747, A:K.747, A:K.773, A:K.773 IHP.3: 8 residues within 4Å: Chain B: T.467, S.468, K.473, K.689, K.721, K.747, K.773, K.775 11 PLIP interactions: 11 interactions with chain B Salt bridges: B:K.473, B:K.689, B:K.689, B:K.721, B:K.721, B:K.721, B:K.747, B:K.747, B:K.773, B:K.773, B:K.775 IHP.5: 8 residues within 4Å: Chain C: T.467, K.473, K.689, N.719, K.721, K.747, K.773, K.775 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.719 Salt bridges: C:K.473, C:K.689, C:K.721, C:K.747, C:K.773, C:K.775, C:K.775 IHP.7: 9 residues within 4Å: Chain D: T.467, S.468, D.469, K.473, K.721, K.747, T.749, K.773, K.775 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.468, D:S.468, D:D.469, D:K.773 Salt bridges: D:K.473, D:K.473, D:K.721, D:K.721, D:K.747, D:K.747, D:K.773, D:K.773, D:K.775 IHP.9: 10 residues within 4Å: Chain E: W.424, T.467, K.473, S.669, K.689, N.719, K.721, K.747, K.773, K.775 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.669 Salt bridges: E:K.473, E:K.473, E:K.689, E:K.689, E:K.721, E:K.721, E:K.747, E:K.773, E:K.775 IHP.11: 9 residues within 4Å: Chain F: T.467, S.468, K.473, K.689, N.719, K.721, K.747, K.773, K.775 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.468 Salt bridges: F:K.473, F:K.473, F:K.473, F:K.689, F:K.721, F:K.721, F:K.747, F:K.747, F:K.773, F:K.775 IHP.13: 10 residues within 4Å: Chain G: T.467, K.473, H.640, K.689, N.719, K.721, I.723, K.747, K.773, K.775 11 PLIP interactions: 11 interactions with chain G Salt bridges: G:K.473, G:H.640, G:K.689, G:K.721, G:K.721, G:K.721, G:K.747, G:K.747, G:K.773, G:K.775, G:K.775 IHP.15: 9 residues within 4Å: Chain H: T.467, K.473, K.689, N.719, K.721, K.747, T.749, K.773, K.775 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:N.719 Salt bridges: H:K.473, H:K.473, H:K.689, H:K.721, H:K.721, H:K.747, H:K.747, H:K.747, H:K.773, H:K.773, H:K.775 IHP.17: 8 residues within 4Å: Chain I: T.467, K.473, K.689, N.719, K.721, K.747, K.773, K.775 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:N.719 Salt bridges: I:K.473, I:K.689, I:K.721, I:K.721, I:K.721, I:K.773, I:K.773, I:K.773, I:K.775 IHP.19: 9 residues within 4Å: Chain J: T.467, Q.471, S.669, K.689, N.719, K.721, K.747, K.773, K.775 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:S.468, J:D.469, J:Q.471, J:S.669, J:N.719 Salt bridges: J:K.473, J:K.689, J:K.689, J:K.721, J:K.721, J:K.721, J:K.747, J:K.747, J:K.773, J:K.775 IHP.21: 9 residues within 4Å: Chain K: T.467, S.468, K.473, H.640, N.719, K.721, K.747, K.773, K.775 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:S.468, K:S.468 Salt bridges: K:K.473, K:H.640, K:K.721, K:K.721, K:K.721, K:K.747, K:K.773, K:K.773, K:K.775, K:K.775 IHP.23: 8 residues within 4Å: Chain L: T.467, K.473, K.689, R.693, K.721, K.747, K.773, K.775 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:R.693 Salt bridges: L:K.473, L:K.689, L:K.721, L:K.721, L:K.747, L:K.773, L:K.773, L:K.773, L:K.775, L:K.775

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

ADP.2: 15 residues within 4Å: Chain A: V.155, V.156, F.158, G.186, L.187, G.188, K.189, T.190, T.191, L.320, P.350, L.351, V.354, M.462, H.478 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.156, A:V.156, A:G.186, A:G.188, A:G.188, A:T.190, A:T.191, A:T.191 Salt bridges: A:K.189, A:H.478, A:H.478 ADP.4: 14 residues within 4Å: Chain B: D.154, V.155, V.156, G.186, G.188, K.189, T.190, T.191, L.320, P.350, L.351, V.354, M.462, H.478 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.154, B:V.156, B:G.186, B:G.188, B:K.189, B:T.190, B:T.190, B:T.190, B:T.191, B:T.191 Salt bridges: B:K.189, B:H.478, B:H.478 ADP.6: 16 residues within 4Å: Chain C: V.155, V.156, F.158, G.186, L.187, G.188, T.191, L.312, L.320, K.324, P.350, L.351, V.354, N.459, M.462, H.478 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.156, C:V.156, C:P.350, C:N.459 Salt bridges: C:K.324, C:K.324 pi-Stacking: C:F.158 ADP.8: 16 residues within 4Å: Chain D: V.155, V.156, F.158, G.186, L.187, G.188, K.189, T.190, T.191, L.312, L.320, P.350, L.351, V.354, M.462, H.478 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:V.156, D:G.186, D:L.187, D:G.188, D:K.189, D:T.190, D:T.190, D:T.190, D:T.190, D:T.191, D:T.191 Salt bridges: D:K.189, D:H.478, D:H.478 ADP.10: 16 residues within 4Å: Chain E: V.155, V.156, F.158, G.186, L.187, G.188, K.189, T.190, T.191, L.312, L.320, K.324, P.350, L.351, V.354, H.478 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:V.156, E:G.186, E:G.188, E:K.189, E:T.190, E:T.191, E:T.191 Salt bridges: E:K.189, E:H.478, E:H.478 pi-Stacking: E:F.158 ADP.12: 15 residues within 4Å: Chain F: V.155, V.156, F.158, G.186, G.188, K.189, T.190, T.191, L.320, K.324, P.350, L.351, V.354, M.462, H.478 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:V.156, F:V.156, F:G.186, F:G.186, F:G.188, F:K.189, F:T.190, F:T.191, F:K.324, F:H.478 Salt bridges: F:K.189, F:H.478 ADP.14: 15 residues within 4Å: Chain G: V.155, V.156, F.158, G.186, L.187, G.188, K.189, T.190, T.191, L.312, L.320, P.350, L.351, M.462, H.478 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.156, G:V.156, G:G.186, G:G.188, G:K.189, G:T.190, G:T.190, G:T.190, G:T.190, G:T.191, G:T.191 Salt bridges: G:K.189, G:H.478, G:H.478 ADP.16: 15 residues within 4Å: Chain H: V.155, V.156, F.158, G.186, G.188, K.189, T.190, T.191, L.320, P.350, L.351, V.354, M.462, R.476, H.478 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:V.156, H:V.156, H:G.186, H:G.188, H:K.189, H:T.190, H:R.476 Salt bridges: H:K.189, H:H.478, H:H.478 pi-Stacking: H:F.158 ADP.18: 15 residues within 4Å: Chain I: V.155, V.156, F.158, G.186, L.187, G.188, K.189, T.190, T.191, L.312, L.320, P.350, L.351, V.354, H.478 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:V.156, I:V.156, I:G.186, I:G.188, I:K.189, I:T.190, I:T.191 Salt bridges: I:K.189, I:H.478, I:H.478 ADP.20: 17 residues within 4Å: Chain J: V.155, V.156, F.158, P.185, G.186, L.187, G.188, K.189, T.190, T.191, L.312, L.320, P.350, L.351, V.354, M.462, H.478 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:V.156, J:V.156, J:G.186, J:L.187, J:G.188, J:K.189, J:T.190, J:T.191, J:T.191 Salt bridges: J:K.189, J:H.478, J:H.478 pi-Stacking: J:F.158 ADP.22: 17 residues within 4Å: Chain K: V.155, V.156, F.158, M.184, P.185, G.186, L.187, G.188, K.189, T.190, T.191, L.320, K.324, P.350, L.351, V.354, H.478 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:V.156, K:V.156, K:M.184, K:G.186, K:G.186, K:L.187, K:G.188, K:K.189, K:T.190, K:T.191, K:T.191 Salt bridges: K:K.189, K:H.478, K:H.478 ADP.24: 15 residues within 4Å: Chain L: V.155, V.156, F.158, P.185, G.186, L.187, G.188, K.189, T.190, T.191, P.350, L.351, V.354, M.462, H.478 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:V.156, L:G.186, L:L.187, L:G.188, L:K.189, L:T.190, L:T.190, L:T.190, L:T.191, L:T.191, L:H.478 Salt bridges: L:K.189, L:H.478, L:H.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, S. et al., Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR. Nature (2024)

Release Date

2024-05-22

Peptides

NRC2: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

NRC2

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