SMTL ID : 6rza.1

Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.50 Å

Oligo State

hetero-1-2-2-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, 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 C: Q.245, K.252 Ligands: MG.2 24 PLIP interactions: 21 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:Q.15, B:D.98, B:A.99, B:A.100, B:N.101, B:S.140, B:G.144, B:T.145, B:T.145, B:T.145, B:G.146, B:E.183, B:N.206, B:Y.224, B:N.228, B:N.228, B:N.228 pi-Stacking: B:Y.224 Salt bridges: C:K.252, C:K.252, C:K.252 GTP.5: 25 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, 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 E: Q.245, K.252 Ligands: MG.6 24 PLIP interactions: 21 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, D:Q.15, D:D.98, D:A.99, D:A.100, D:N.101, D:S.140, D:G.144, D:T.145, D:T.145, D:T.145, D:G.146, D:E.183, D:N.206, D:Y.224, D:N.228, D:N.228, D:N.228 pi-Stacking: D:Y.224 Salt bridges: E:K.252, E:K.252, E:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: Q.11, D.69, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 MG.6: 4 residues within 4Å: Chain D: Q.11, D.69, E.71 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.71

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

GDP.3: 15 residues within 4Å: Chain C: 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 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:N.99, C:S.138, C:G.142, C:T.143, C:G.144, C:D.177, C:E.181, C:N.204, C:Y.222, C:N.226, C:N.226, C:N.226 pi-Stacking: C:Y.222, C:Y.222 GDP.7: 15 residues within 4Å: Chain E: 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 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Q.11, E:Q.11, E:C.12, E:N.99, E:S.138, E:G.142, E:T.143, E:G.144, E:D.177, E:E.181, E:N.204, E:Y.222, E:N.226, E:N.226, E:N.226 pi-Stacking: E:Y.222, E:Y.222

2 x TA1: TAXOL(Non-covalent)

TA1.4: 20 residues within 4Å: Chain C: 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 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:E.22, C:V.23, C:D.26, C:L.215, C:H.227, C:L.228, C:A.231, C:F.270, C:R.276, C:P.358, C:L.361 Hydrogen bonds: C:T.274, C:R.359 Salt bridges: C:H.227, C:R.276 pi-Stacking: C:H.227 pi-Cation interactions: C:K.19 TA1.8: 21 residues within 4Å: Chain E: 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, Q.279, R.318, P.358, R.359, G.360, L.361 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:E.22, E:V.23, E:D.26, E:L.215, E:H.227, E:L.228, E:A.231, E:F.270, E:R.276, E:P.358, E:L.361 Hydrogen bonds: E:T.274, E:Q.279, E:R.359 Salt bridges: E:H.227, E:R.276 pi-Stacking: E:H.227 pi-Cation interactions: E: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

Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal,Cytoplasmic dynein 1 heavy chain 1: A
Tubulin alpha-1B chain: BD
Tubulin beta chain: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
A

D
C

C
B

E
D

Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal,Cytoplasmic dynein 1 heavy chain 1

Tubulin alpha-1B chain

Tubulin beta chain

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