SMTL ID : 6rzb.1

Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 5.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 26 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, N.206, Y.224, L.227, N.228 Chain B: Q.245, K.252 Ligands: MG.2 23 PLIP interactions: 3 interactions with chain B, 20 interactions with chain A Salt bridges: B:K.252, B:K.252, B:K.252 Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224 pi-Cation interactions: A:Y.224

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.69, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71

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

GDP.3: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222

1 x TA1: TAXOL(Non-covalent)

TA1.4: 20 residues within 4Å: Chain B: K.19, E.22, V.23, D.26, L.215, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, R.276, R.318, P.358, R.359, G.360, L.361 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:E.22, B:V.23, B:V.23, B:D.26, B:L.215, B:H.227, B:L.228, B:A.231, B:F.270, B:R.276, B:P.358, B:L.361 Hydrogen bonds: B:D.26, B:T.274, B:R.359 Salt bridges: B:H.227, B:R.276 pi-Stacking: B:H.227 pi-Cation interactions: B:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lacey, S.E. et al., Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule. Elife (2019)

Release Date

2019-07-10

Peptides

Tubulin alpha-1B chain: A
Tubulin beta chain: B
MKIAA0325 protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tubulin alpha-1B chain

Tubulin beta chain

MKIAA0325 protein

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