SMTL ID : 8vh4.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

GDP.1: 11 residues within 4Å: Chain A: G.1344, S.1345, K.1347, T.1348, T.1349, T.1368, T.1452, H.1453, D.1455, N.1489, T.1491 9 PLIP interactions: 9 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.1491 Salt bridges: A:K.1347, A:D.1455

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

ANP.2: 15 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, N.1999, 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:S.1954, A:H.1998

1 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

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

GNP.4: 20 residues within 4Å: Chain B: R.16, G.17, V.18, G.19, K.20, T.21, S.22, E.34, C.36, S.38, T.39, T.63, A.64, N.120, K.121, D.123, S.151, A.152, K.153 Ligands: MG.3 20 PLIP interactions: 20 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.63, B:N.120, B:K.121, B:A.152, B:K.153 Salt bridges: B:D.123 pi-Stacking: B: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: A
Ras-related protein Rab-12: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Leucine-rich repeat serine/threonine-protein kinase 2

Ras-related protein Rab-12

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