SMTL ID : 8fo9.1

Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 tetramer state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

GDP.1: 16 residues within 4Å: Chain A: T.1343, G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, Q.1365, S.1366, A.1367, T.1368, A.1396, G.1397, R.1398, H.1453, A.1490 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.1343, A:G.1344, A:G.1346, A:K.1347, A:T.1348, A:T.1348, A:Q.1365, A:T.1368, A:T.1368, A:T.1368, A:G.1397 pi-Stacking: A:H.1453 pi-Cation interactions: A:H.1453 GDP.3: 16 residues within 4Å: Chain B: T.1343, G.1344, S.1345, G.1346, K.1347, T.1348, T.1349, Q.1365, S.1366, A.1367, T.1368, A.1396, G.1397, R.1398, H.1453, A.1490 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.1343, B:G.1344, B:G.1346, B:K.1347, B:T.1348, B:T.1348, B:Q.1365, B:T.1368, B:T.1368, B:T.1368, B:G.1397 pi-Stacking: B:H.1453 pi-Cation interactions: B:H.1453 GDP.5: 15 residues within 4Å: Chain E: G.1344, S.1345, K.1347, T.1348, T.1349, Q.1365, A.1367, T.1368, G.1397, T.1452, H.1453, D.1455, N.1489, A.1490, T.1491 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.1344, E:S.1345, E:K.1347, E:T.1348, E:Q.1365, E:T.1368, E:T.1368, E:G.1397, E:T.1491 Salt bridges: E:D.1455 pi-Cation interactions: E:H.1453 GDP.7: 15 residues within 4Å: Chain F: G.1344, S.1345, K.1347, T.1348, T.1349, Q.1365, A.1367, T.1368, G.1397, T.1452, H.1453, D.1455, N.1489, A.1490, T.1491 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.1344, F:S.1345, F:K.1347, F:T.1348, F:Q.1365, F:T.1368, F:T.1368, F:G.1397 Salt bridges: F:D.1455 pi-Cation interactions: F:H.1453

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 18 residues within 4Å: Chain A: L.1885, D.1887, V.1893, A.1904, I.1933, M.1947, E.1948, L.1949, A.1950, S.1951, G.1953, S.1954, R.1957, H.1998, N.1999, L.2001, A.2016, D.2017 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.1887, A:D.1887, A:A.1950, A:S.1954, A:S.1954 pi-Cation interactions: A:R.1895 ATP.4: 18 residues within 4Å: Chain B: L.1885, D.1887, V.1893, A.1904, I.1933, M.1947, E.1948, L.1949, A.1950, S.1951, G.1953, S.1954, R.1957, H.1998, N.1999, L.2001, A.2016, D.2017 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.1887, B:D.1887, B:A.1950, B:S.1954, B:S.1954 pi-Cation interactions: B:R.1895 ATP.6: 11 residues within 4Å: Chain E: D.1887, G.1888, V.1893, A.1904, M.1947, E.1948, A.1950, S.1954, R.1957, H.1998, L.2001 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:E.1948, E:A.1950, E:S.1954, E:H.1998 Salt bridges: E:K.1906, E:H.1998 ATP.8: 11 residues within 4Å: Chain F: D.1887, G.1888, V.1893, A.1904, M.1947, E.1948, A.1950, S.1954, R.1957, H.1998, L.2001 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.1948, F:A.1950, F:S.1954, F:H.1998 Salt bridges: F:K.1906, F:H.1998

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science (2023)

Release Date

2024-01-03

Peptides

Leucine-rich repeat serine/threonine-protein kinase 2: ABEF
Ras-related protein Rab-7L1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

E
E

F
F

C
B

D
D

Leucine-rich repeat serine/threonine-protein kinase 2

Ras-related protein Rab-7L1

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