SMTL ID : 6z1f.1

CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-8-8-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, I.187, I.191, I.214, D.215, S.218 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.3, A:R.37, A:G.39, A:E.40, A:G.41, A:K.42, A:T.43, A:T.43, A:T.43, A:F.44, A:D.215, A:D.215, A:S.218 Salt bridges: A:K.42 pi-Stacking: A:F.44, A:F.44

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 21 residues within 4Å: Chain B: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, I.187, I.191, I.214, D.215, S.218 Chain C: R.27, P.165, R.168, R.171 Ligands: MG.3 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:R.27, C:R.168, C:R.171, B:Y.3, B:G.39, B:E.40, B:G.41, B:K.42, B:K.42, B:T.43, B:T.43, B:T.43, B:F.44, B:S.218 Salt bridges: C:R.168, C:R.168, B:K.42 pi-Stacking: B:F.44, B:F.44 AGS.4: 21 residues within 4Å: Chain C: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, I.187, I.191, I.214, D.215, S.218 Chain D: R.27, P.165, R.168, R.171 Ligands: MG.5 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.3, C:G.39, C:E.40, C:G.41, C:K.42, C:K.42, C:T.43, C:T.43, C:T.43, C:F.44, C:S.218, D:R.27, D:R.27, D:R.171 Salt bridges: C:K.42, D:R.168, D:R.168 AGS.6: 21 residues within 4Å: Chain D: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, T.155, I.187, I.191, I.214, D.215, S.218 Chain E: R.27, R.168, R.171 Ligands: MG.7 15 PLIP interactions: 5 interactions with chain E, 10 interactions with chain D Hydrogen bonds: E:R.27, E:R.27, E:R.171, D:Y.3, D:G.39, D:E.40, D:G.41, D:K.42, D:T.43, D:T.43, D:F.44, D:S.218 Salt bridges: E:R.168, E:R.168, D:K.42 AGS.8: 22 residues within 4Å: Chain E: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, I.187, I.191, I.214, D.215, S.218 Chain F: R.27, D.131, P.165, R.168, R.171 Ligands: MG.9 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Y.3, E:G.39, E:E.40, E:G.41, E:K.42, E:K.42, E:T.43, E:T.43, E:F.44, E:S.218, F:R.27, F:R.171 Salt bridges: E:K.42, F:R.168 AGS.10: 21 residues within 4Å: Chain A: R.168 Chain F: Y.2, Y.3, R.37, K.38, G.39, E.40, G.41, K.42, T.43, F.44, Q.45, N.100, D.101, T.155, N.157, I.187, I.191, I.214, D.215, S.218 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:Y.3, F:G.39, F:E.40, F:G.41, F:K.42, F:K.42, F:T.43, F:F.44, F:N.157, F:S.218, A:R.168 Salt bridges: F:K.42, A:R.168, A:R.168 pi-Stacking: F:F.44, F:F.44

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.43 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.43 MG.5: 5 residues within 4Å: Chain C: T.43, N.100 Chain D: D.131, R.171 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.43 MG.7: 3 residues within 4Å: Chain D: T.43 Chain E: R.168 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.43 MG.9: 3 residues within 4Å: Chain E: T.43 Chain F: D.131 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.43 MG.11: 4 residues within 4Å: Chain G: K.202, D.204, E.205 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.204, G:E.205 MG.13: 3 residues within 4Å: Chain H: K.202, D.204, E.205 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.205 MG.14: 5 residues within 4Å: Chain I: K.176, K.202, D.204, E.205 Ligands: CAP.15 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.204, I:E.205 MG.16: 5 residues within 4Å: Chain J: K.176, K.202, D.204, E.205 Ligands: CAP.17 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.204, J:E.205 MG.18: 6 residues within 4Å: Chain K: K.176, K.178, K.202, D.204, E.205 Ligands: CAP.19 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.204, K:E.205 MG.20: 6 residues within 4Å: Chain L: K.176, K.178, K.202, D.204, E.205 Ligands: CAP.21 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.204, L:E.205 MG.22: 6 residues within 4Å: Chain M: K.176, K.178, K.202, D.204, E.205 Ligands: CAP.23 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.204, M:E.205 MG.24: 6 residues within 4Å: Chain N: K.176, K.178, K.202, D.204, E.205 Ligands: CAP.25 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.204, N:E.205

7 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.12: 23 residues within 4Å: Chain G: T.174, K.176, K.178, K.202, D.204, E.205, H.295, R.296, H.299, H.328, G.330, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain H: E.61, T.66, W.67, N.124 Ligands: MG.11 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:T.174, G:K.176, G:E.205, G:G.382, G:G.404, G:G.405, H:N.124 Salt bridges: G:K.176, G:K.176, G:K.178, G:R.296, G:H.328, G:K.335, G:K.335 CAP.15: 18 residues within 4Å: Chain I: K.176, K.202, E.205, H.295, R.296, H.328, G.330, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain J: E.61, W.67, N.124 Ligands: MG.14 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:K.176, I:E.205, I:E.205, I:G.382, I:G.404, I:G.405, J:N.124 Salt bridges: I:K.176, I:K.176, I:K.178, I:R.296, I:H.328, I:K.335, I:K.335 CAP.17: 18 residues within 4Å: Chain I: E.61, W.67, N.124 Chain J: K.176, K.202, E.205, H.295, R.296, H.328, G.330, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.16 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:K.176, J:E.205, J:S.380, J:G.382, J:G.404, J:G.405, I:N.124 Salt bridges: J:K.176, J:K.176, J:K.178, J:R.296, J:H.328, J:K.335, J:K.335 CAP.19: 19 residues within 4Å: Chain K: K.176, K.178, K.202, E.205, H.295, R.296, H.299, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain L: E.61, W.67, N.124 Ligands: MG.18 14 PLIP interactions: 12 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:K.176, K:E.205, K:G.382, K:G.404, K:G.405, L:E.61, L:N.124 Salt bridges: K:K.176, K:K.176, K:K.178, K:R.296, K:H.328, K:K.335, K:K.335 CAP.21: 18 residues within 4Å: Chain K: E.61, W.67, N.124 Chain L: K.176, K.202, E.205, H.295, R.296, H.299, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.20 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:K.176, L:H.299, L:G.382, L:G.404, L:G.405, K:N.124 Salt bridges: L:K.176, L:K.176, L:K.178, L:R.296, L:H.328, L:K.335, L:K.335 CAP.23: 18 residues within 4Å: Chain M: K.176, K.202, E.205, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Chain N: E.61, T.66, W.67, N.124 Ligands: MG.22 14 PLIP interactions: 12 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:K.176, M:E.205, M:G.382, M:G.404, M:G.405, N:E.61, N:N.124 Salt bridges: M:K.176, M:K.176, M:K.178, M:R.296, M:H.328, M:K.335, M:K.335 CAP.25: 18 residues within 4Å: Chain M: E.61, W.67, N.124 Chain N: K.176, K.178, K.202, E.205, H.295, R.296, H.328, K.335, L.336, S.380, G.381, G.382, G.404, G.405 Ligands: MG.24 12 PLIP interactions: 11 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:K.176, N:G.382, N:G.404, N:G.405, M:N.124 Salt bridges: N:K.176, N:K.176, N:K.178, N:R.296, N:H.328, N:K.335, N:K.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flecken, M. et al., Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes. Cell (2020)

Release Date

2020-09-23

Peptides

Ribulose bisphosphate carboxylase/oxygenase activase: ABCDEF
Ribulose bisphosphate carboxylase large chain: GHIJKLMN
Ribulose bisphosphate carboxylase small chain: OPQRSTUV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

O
I

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

Ribulose bisphosphate carboxylase/oxygenase activase

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain

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