SMTL ID : 7yyo.1

Cryo-EM structure of an a-carboxysome RuBisCO enzyme at 2.9 A resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: G.373, H.378 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.373, A:H.378 MG.3: 2 residues within 4Å: Chain C: G.373, H.378 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:G.373, C:H.378 MG.5: 2 residues within 4Å: Chain E: G.373, H.378 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:G.373, E:H.378 MG.7: 2 residues within 4Å: Chain G: G.373, H.378 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:G.373, G:H.378 MG.9: 2 residues within 4Å: Chain I: G.373, H.378 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:G.373, I:H.378 MG.11: 2 residues within 4Å: Chain K: G.373, H.378 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:G.373, K:H.378 MG.13: 2 residues within 4Å: Chain M: G.373, H.378 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:G.373, M:H.378 MG.15: 2 residues within 4Å: Chain O: G.373, H.378 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:G.373, O:H.378

8 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Covalent)

CAP.2: 9 residues within 4Å: Chain A: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 Chain O: S.59 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain O Hydrogen bonds: A:G.373, A:G.395, A:G.395, A:G.396, A:G.397, O:S.59, O:S.59 CAP.4: 9 residues within 4Å: Chain C: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 Chain M: S.59 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain M Hydrogen bonds: C:G.373, C:G.395, C:G.395, C:G.396, C:G.397, M:S.59, M:S.59 CAP.6: 9 residues within 4Å: Chain E: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 Chain K: S.59 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain K Hydrogen bonds: E:G.373, E:G.395, E:G.395, E:G.396, E:G.397, K:S.59, K:S.59 CAP.8: 9 residues within 4Å: Chain G: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 Chain I: S.59 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain I Hydrogen bonds: G:G.373, G:G.395, G:G.395, G:G.396, G:G.397, I:S.59, I:S.59 CAP.10: 9 residues within 4Å: Chain G: S.59 Chain I: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain I Hydrogen bonds: G:S.59, G:S.59, I:G.373, I:G.396, I:G.396, I:G.397 CAP.12: 9 residues within 4Å: Chain E: S.59 Chain K: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain K Hydrogen bonds: E:S.59, E:T.60, E:T.60, K:G.373, K:G.396, K:G.396, K:G.397 CAP.14: 9 residues within 4Å: Chain C: S.59 Chain M: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 5 PLIP interactions: 4 interactions with chain M, 1 interactions with chain C Hydrogen bonds: M:G.373, M:G.396, M:G.396, M:G.397, C:S.59 CAP.16: 9 residues within 4Å: Chain A: S.59 Chain O: K.167, G.373, F.394, G.395, G.396, G.397, G.400, W.454 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain A Hydrogen bonds: O:G.373, O:G.396, O:G.396, O:G.397, A:S.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, S.L. et al., Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact alpha-carboxysome. Structure (2023)

Release Date

2023-01-25

Peptides

Ribulose bisphosphate carboxylase large chain: ACEGIKMO
Ribulose bisphosphate carboxylase small chain: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

Ribulose bisphosphate carboxylase large chain

Ribulose bisphosphate carboxylase small chain

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