SMTL ID : 7n32.1

protofilaments of microtubule doublets bound to outer-arm dynein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.50 Å

Oligo State

hetero-12-12-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, G.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain B: Q.245, L.246, K.252 Ligands: MG.2 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:G.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:T.179, A:N.206, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.4: 23 residues within 4Å: Chain C: G.10, Q.11, G.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain D: Q.245, L.246, K.252 Ligands: MG.5 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:G.12, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:T.179, C:N.206, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252, D:K.252 GTP.7: 26 residues within 4Å: Chain E: G.10, Q.11, G.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain F: Q.245, L.246, K.252 Ligands: MG.8 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Q.11, E:G.12, E:A.99, E:A.100, E:S.140, E:G.144, E:T.145, E:T.145, E:G.146, E:T.179, E:N.206, E:N.228, E:N.228, E:N.228 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: F:K.252, F:K.252, F:K.252 GTP.10: 23 residues within 4Å: Chain G: G.10, Q.11, G.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain H: Q.245, L.246, K.252 Ligands: MG.11 20 PLIP interactions: 17 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:Q.11, G:G.12, G:A.99, G:A.100, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, G:T.179, G:N.206, G:N.228, G:N.228, G:N.228 pi-Stacking: G:Y.224, G:Y.224 Salt bridges: H:K.252, H:K.252, H:K.252 GTP.13: 25 residues within 4Å: Chain I: G.10, Q.11, G.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain J: Q.245, L.246, K.252 Ligands: MG.14 19 PLIP interactions: 16 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:Q.11, I:G.12, I:A.99, I:A.100, I:S.140, I:G.144, I:T.145, I:T.145, I:G.146, I:T.179, I:N.206, I:N.228, I:N.228, I:N.228 pi-Stacking: I:Y.224, I:Y.224 Salt bridges: J:K.252, J:K.252, J:K.252 GTP.16: 24 residues within 4Å: Chain K: G.10, Q.11, G.12, Q.15, V.16, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain L: Q.245, L.246, K.252 Ligands: MG.17 20 PLIP interactions: 17 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:Q.11, K:G.12, K:A.99, K:A.100, K:N.101, K:S.140, K:G.144, K:T.145, K:T.145, K:G.146, K:T.179, K:N.206, K:N.228, K:N.228, K:N.228 pi-Stacking: K:Y.224, K:Y.224 Salt bridges: L:K.252, L:K.252, L:K.252 GTP.19: 26 residues within 4Å: Chain M: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain N: Q.245, L.246, K.252 Ligands: MG.20 21 PLIP interactions: 18 interactions with chain M, 3 interactions with chain N Hydrogen bonds: M:Q.11, M:G.12, M:A.99, M:A.100, M:N.101, M:S.140, M:G.144, M:T.145, M:T.145, M:G.146, M:T.179, M:T.179, M:N.206, M:N.228, M:N.228, M:N.228 pi-Stacking: M:Y.224, M:Y.224 Salt bridges: N:K.252, N:K.252, N:K.252 GTP.22: 25 residues within 4Å: Chain O: G.10, Q.11, G.12, Q.15, V.16, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain P: Q.245, L.246, K.252 Ligands: MG.23 21 PLIP interactions: 18 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:Q.11, O:G.12, O:A.99, O:A.100, O:N.101, O:S.140, O:G.144, O:T.145, O:T.145, O:G.146, O:T.179, O:T.179, O:N.206, O:N.228, O:N.228, O:N.228 pi-Stacking: O:Y.224, O:Y.224 Salt bridges: P:K.252, P:K.252, P:K.252 GTP.25: 23 residues within 4Å: Chain Q: G.10, Q.11, G.12, Q.15, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain R: Q.245, L.246, K.252 Ligands: MG.26 21 PLIP interactions: 18 interactions with chain Q, 3 interactions with chain R Hydrogen bonds: Q:Q.11, Q:G.12, Q:A.99, Q:A.100, Q:N.101, Q:S.140, Q:G.144, Q:T.145, Q:T.145, Q:G.146, Q:T.179, Q:T.179, Q:N.206, Q:N.228, Q:N.228, Q:N.228 pi-Stacking: Q:Y.224, Q:Y.224 Salt bridges: R:K.252, R:K.252, R:K.252 GTP.28: 23 residues within 4Å: Chain S: G.10, Q.11, G.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain V: Q.245, L.246, K.252 Ligands: MG.29 22 PLIP interactions: 19 interactions with chain S, 3 interactions with chain V Hydrogen bonds: S:Q.11, S:G.12, S:A.99, S:A.100, S:N.101, S:S.140, S:G.144, S:T.145, S:T.145, S:T.145, S:G.146, S:T.179, S:T.179, S:N.206, S:N.228, S:N.228, S:N.228 pi-Stacking: S:Y.224, S:Y.224 Salt bridges: V:K.252, V:K.252, V:K.252 GTP.30: 24 residues within 4Å: Chain T: G.10, Q.11, G.12, Q.15, D.69, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain U: Q.245, L.246, K.252 Ligands: MG.31 21 PLIP interactions: 18 interactions with chain T, 3 interactions with chain U Hydrogen bonds: T:Q.11, T:G.12, T:A.99, T:A.100, T:N.101, T:S.140, T:G.144, T:T.145, T:T.145, T:G.146, T:T.179, T:T.179, T:N.206, T:N.228, T:N.228, T:N.228 pi-Stacking: T:Y.224, T:Y.224 Salt bridges: U:K.252, U:K.252, U:K.252 GTP.33: 26 residues within 4Å: Chain W: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain X: Q.245, L.246, K.252 Ligands: MG.34 22 PLIP interactions: 19 interactions with chain W, 3 interactions with chain X Hydrogen bonds: W:Q.11, W:G.12, W:A.99, W:A.100, W:N.101, W:S.140, W:G.144, W:T.145, W:T.145, W:T.145, W:G.146, W:T.179, W:T.179, W:N.206, W:N.228, W:N.228, W:N.228 pi-Stacking: W:Y.224, W:Y.224 Salt bridges: X:K.252, X:K.252, X:K.252

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: Q.11, E.71 Chain D: K.252 Ligands: GTP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.8: 4 residues within 4Å: Chain E: Q.11, E.71 Chain F: K.252 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain G: Q.11, E.71 Chain H: K.252 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.71 MG.14: 3 residues within 4Å: Chain I: Q.11 Chain J: K.252 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain K: Q.11, D.69, E.71 Chain L: K.252 Ligands: GTP.16 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.71 MG.20: 4 residues within 4Å: Chain M: Q.11, E.71 Chain N: K.252 Ligands: GTP.19 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:E.71 MG.23: 4 residues within 4Å: Chain O: Q.11, E.71 Chain P: K.252 Ligands: GTP.22 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:E.71 MG.26: 3 residues within 4Å: Chain Q: E.71 Chain R: K.252 Ligands: GTP.25 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.71 MG.29: 4 residues within 4Å: Chain S: Q.11, E.71 Chain V: K.252 Ligands: GTP.28 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain T: E.71 Chain U: K.252 Ligands: GTP.30 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.71 MG.34: 3 residues within 4Å: Chain W: E.71 Chain X: K.252 Ligands: GTP.33 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.71

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

GDP.3: 14 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, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:E.181, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.6: 17 residues within 4Å: Chain A: L.248 Chain D: G.10, Q.11, C.12, Q.15, D.67, S.138, G.141, G.142, T.143, G.144, D.177, T.178, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:T.143, D:G.144, D:T.178, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.9: 15 residues within 4Å: Chain C: L.248 Chain F: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:T.143, F:G.144, F:D.177, F:E.181, F:N.204, F:N.204, F:Y.222, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 GDP.12: 14 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:S.138, H:G.141, H:G.142, H:T.143, H:T.143, H:T.143, H:T.143, H:G.144, H:T.178, H:T.178, H:N.204, H:N.204, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GDP.15: 15 residues within 4Å: Chain G: L.248 Chain J: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:S.138, J:G.141, J:G.142, J:T.143, J:T.143, J:T.143, J:T.143, J:G.144, J:E.181, J:N.204, J:N.204, J:Y.222, J:N.226, J:N.226 pi-Stacking: J:Y.222, J:Y.222 GDP.18: 15 residues within 4Å: Chain I: L.248 Chain L: 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 18 PLIP interactions: 18 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:N.99, L:S.138, L:G.141, L:G.142, L:T.143, L:G.144, L:D.177, L:D.177, L:E.181, L:N.204, L:N.204, L:Y.222, L:N.226, L:N.226 pi-Stacking: L:Y.222, L:Y.222 GDP.21: 14 residues within 4Å: Chain N: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:D.67, N:S.138, N:G.141, N:G.142, N:T.143, N:T.143, N:T.143, N:G.144, N:E.181, N:E.181, N:N.204, N:N.204, N:N.226, N:N.226 pi-Stacking: N:Y.222, N:Y.222 GDP.24: 15 residues within 4Å: Chain P: G.10, Q.11, C.12, Q.15, D.67, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Chain W: L.248 22 PLIP interactions: 22 interactions with chain P Hydrogen bonds: P:Q.11, P:C.12, P:S.138, P:G.141, P:G.142, P:T.143, P:T.143, P:T.143, P:T.143, P:G.144, P:D.177, P:D.177, P:T.178, P:T.178, P:E.181, P:N.204, P:N.204, P:Y.222, P:N.226, P:N.226 pi-Stacking: P:Y.222, P:Y.222 GDP.27: 14 residues within 4Å: Chain R: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 19 PLIP interactions: 19 interactions with chain R Hydrogen bonds: R:Q.11, R:Q.11, R:C.12, R:S.138, R:G.141, R:G.142, R:T.143, R:T.143, R:T.143, R:T.143, R:G.144, R:E.181, R:E.181, R:N.204, R:N.204, R:N.226, R:N.226 pi-Stacking: R:Y.222, R:Y.222 GDP.32: 15 residues within 4Å: Chain S: L.248 Chain U: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 20 PLIP interactions: 20 interactions with chain U Hydrogen bonds: U:Q.11, U:C.12, U:N.99, U:S.138, U:G.141, U:G.142, U:T.143, U:T.143, U:T.143, U:T.143, U:G.144, U:E.181, U:E.181, U:N.204, U:N.204, U:Y.222, U:Y.222, U:N.226 pi-Stacking: U:Y.222, U:Y.222 GDP.35: 14 residues within 4Å: Chain M: L.248 Chain X: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain X Hydrogen bonds: X:Q.11, X:C.12, X:D.67, X:S.138, X:G.142, X:T.143, X:T.143, X:T.143, X:G.144, X:E.181, X:E.181, X:N.204, X:N.204, X:Y.222, X:N.226, X:N.226 pi-Stacking: X:Y.222, X:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, Q. et al., Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-29

Peptides

Tubulin alpha chain: ACEGIKMOQSTW
Tubulin beta chain: BDFHJLNPRUVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
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E
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G
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K
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Tubulin alpha chain

Tubulin beta chain

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