SMTL ID : 8vh5.1

Cryo-EM structure of Rab12-LRRK2 complex in the LRRK2 dimer state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 13 residues within 4Å: Chain A: T.1343, G.1344, S.1345, K.1347, T.1348, T.1349, A.1367, T.1368, T.1452, H.1453, D.1455, N.1489, T.1491 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.1344, A:S.1345, A:K.1347, A:T.1348, A:T.1349, A:T.1368, A:T.1368 Salt bridges: A:K.1347, A:D.1455 pi-Cation interactions: A:H.1453 GDP.5: 13 residues within 4Å: Chain C: T.1343, G.1344, S.1345, K.1347, T.1348, T.1349, A.1367, T.1368, T.1452, H.1453, D.1455, N.1489, T.1491 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.1344, C:S.1345, C:K.1347, C:T.1348, C:T.1349, C:T.1368, C:T.1368 Salt bridges: C:K.1347, C:D.1455 pi-Cation interactions: C:H.1453

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 14 residues within 4Å: Chain A: D.1887, G.1888, F.1890, G.1891, V.1893, A.1904, K.1906, M.1947, E.1948, L.1949, A.1950, S.1954, H.1998, L.2001 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.1890, A:G.1891, A:E.1948, A:A.1950, A:H.1998, A:H.1998 ANP.6: 14 residues within 4Å: Chain C: D.1887, G.1888, F.1890, G.1891, V.1893, A.1904, K.1906, M.1947, E.1948, L.1949, A.1950, S.1954, H.1998, L.2001 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.1890, C:G.1891, C:E.1948, C:A.1950, C:H.1998, C:H.1998

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.21 Ligands: GNP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.21 MG.7: 2 residues within 4Å: Chain D: T.21 Ligands: GNP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.21

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.4: 23 residues within 4Å: Chain B: S.15, R.16, G.17, V.18, G.19, K.20, T.21, S.22, F.32, E.34, C.36, S.38, T.39, D.62, T.63, A.64, N.120, K.121, D.123, S.151, A.152, K.153 Ligands: MG.3 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.17, B:V.18, B:G.19, B:K.20, B:K.20, B:T.21, B:T.21, B:S.22, B:S.22, B:E.34, B:C.36, B:C.36, B:T.39, B:T.39, B:T.39, B:T.39, B:N.120, B:K.121, B:S.151, B:A.152, B:K.153 Salt bridges: B:D.123 pi-Stacking: B:F.32, B:F.32 GNP.8: 23 residues within 4Å: Chain D: S.15, R.16, G.17, V.18, G.19, K.20, T.21, S.22, F.32, E.34, C.36, S.38, T.39, D.62, T.63, A.64, N.120, K.121, D.123, S.151, A.152, K.153 Ligands: MG.7 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:G.17, D:V.18, D:G.19, D:K.20, D:K.20, D:T.21, D:T.21, D:S.22, D:S.22, D:E.34, D:C.36, D:C.36, D:T.39, D:T.39, D:T.39, D:T.39, D:N.120, D:K.121, D:S.151, D:A.152, D:K.153 Salt bridges: D:D.123 pi-Stacking: D:F.32, D:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., RAB12-LRRK2 complex suppresses primary ciliogenesis and regulates centrosome homeostasis in astrocytes. Nat Commun (2024)

Release Date

2024-10-09

Peptides

Leucine-rich repeat serine/threonine-protein kinase 2: AC
Ras-related protein Rab-12: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Leucine-rich repeat serine/threonine-protein kinase 2

Ras-related protein Rab-12

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