SMTL ID : 6u0t.1

Protofilament Ribbon Flagellar Proteins Rib43a-S

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-1-mer

Ligands

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

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

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: A.99, T.145 Ligands: GTP.4 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain E: Q.11, E.71, T.145 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.71 MG.11: 4 residues within 4Å: Chain G: D.69, E.71, T.145 Ligands: GTP.10 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.71, G:E.71 MG.14: 2 residues within 4Å: Chain I: E.71 Ligands: GTP.13 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.71, I:E.71 MG.17: 3 residues within 4Å: Chain K: E.71, T.145 Ligands: GTP.16 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.71, K:E.71

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

GDP.3: 13 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.141, B:T.143, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222 GDP.6: 14 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, E.69, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:E.69, D:S.138, D:T.143, D:G.144, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222 GDP.9: 14 residues within 4Å: Chain F: G.10, Q.11, C.12, E.69, S.138, G.141, G.142, T.143, G.144, N.204, L.207, Y.222, L.225, N.226 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:E.69, F:S.138, F:G.141, F:T.143, F:G.144, F:N.204, F:N.204, F:Y.222, F:N.226 pi-Cation interactions: F:Y.222 GDP.12: 15 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, D.67, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:Q.11, H:C.12, H:S.138, H:T.143, H:T.143, H:T.143, H:G.144, H:D.177, H:N.204, H:N.204, H:Y.222, H:Y.222, H:N.226 pi-Stacking: H:Y.222 GDP.15: 14 residues within 4Å: Chain G: L.248, E.254 Chain J: Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:S.138, J:G.141, J:T.143, J:T.143, J:G.144, J:D.177, J:E.181, J:N.204, J:N.226, J:N.226, J:N.226 pi-Stacking: J:Y.222 GDP.18: 17 residues within 4Å: Chain I: E.254 Chain L: G.10, Q.11, C.12, E.69, A.97, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 Chain M: Y.8 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain M Hydrogen bonds: L:Q.11, L:Q.11, L:C.12, L:E.69, L:S.138, L:G.142, L:T.143, L:T.143, L:G.144, L:D.177, L:E.181, L:N.204, L:N.204, L:Y.222, L:N.226, M:Y.8 pi-Stacking: L:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ichikawa, M. et al., Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-25

Peptides

Tubulin alpha chain: ACEGIK
Tubulin beta chain: BDFHJL
RIB43A protein: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
D

E
E

G
F

I
G

K
H

B
B

D
I

F
J

H
K

J
L

L
M

M
A

Tubulin alpha chain

Tubulin beta chain

RIB43A protein

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