SMTL ID : 6u0u.1

Protofilament Ribbon Flagellar Proteins Rib43a-L

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, 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 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:E.183, 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: 22 residues within 4Å: Chain C: G.10, Q.11, G.12, Q.15, V.16, D.69, E.71, A.99, N.101, S.140, G.143, G.144, T.145, G.146, T.179, N.206, Y.224, L.227, N.228 Chain D: L.246, K.252 Ligands: MG.5 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:G.12, C:E.71, C:E.71, C:A.99, C:N.101, 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 Salt bridges: D:K.252, D:K.252, D:K.252 GTP.7: 25 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, 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 H: 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 I: K.252 Ligands: MG.11 19 PLIP interactions: 16 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:Q.11, H:G.12, H:D.98, H:A.99, H:A.100, H:S.140, H:G.144, H:T.145, H:G.146, H:T.179, H:E.183, H:Y.224, H:N.228, H:N.228, H:N.228 pi-Cation interactions: H:Y.224 Salt bridges: I:K.252, I:K.252, I:K.252 GTP.13: 22 residues within 4Å: Chain J: 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, I.171, T.179, E.183, N.206, Y.224, N.228 Chain K: L.246, K.252 Ligands: MG.14 21 PLIP interactions: 17 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:Q.11, J:G.12, J:A.99, J:A.100, J:N.101, J:S.140, J:G.144, J:T.145, J:E.183, J:N.206, J:N.206, J:Y.224, J:N.228, J:N.228, K:N.247 pi-Stacking: J:Y.224, J:Y.224 pi-Cation interactions: J:Y.224 Salt bridges: K:K.252, K:K.252, K:K.252 GTP.16: 24 residues within 4Å: Chain L: Q.11, G.12, Q.15, V.16, E.71, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain M: N.247, K.252 Ligands: MG.17 23 PLIP interactions: 20 interactions with chain L, 3 interactions with chain M Hydrogen bonds: L:Q.11, L:G.12, L:D.98, L:A.99, L:A.100, L:N.101, L:S.140, L:G.143, L:G.144, L:T.145, L:T.179, L:E.183, L:N.206, L:Y.224, L:Y.224, L:N.228, L:N.228, L:N.228 pi-Stacking: L:Y.224, L:Y.224 Salt bridges: M:K.252, M:K.252, M: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: 3 residues within 4Å: Chain E: Q.11, E.71 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.71 MG.11: 4 residues within 4Å: Chain H: Q.11, D.69, E.71 Ligands: GTP.10 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.71 MG.14: 3 residues within 4Å: Chain J: E.71, T.145 Ligands: GTP.13 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.71, J:E.71 MG.17: 3 residues within 4Å: Chain L: E.71, T.145 Ligands: GTP.16 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.71

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

GDP.3: 14 residues within 4Å: Chain B: 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:E.69, B:S.138, B:T.143, B:T.143, B:G.144, B:D.177, 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: 13 residues within 4Å: Chain F: G.10, Q.11, C.12, S.138, G.141, G.142, T.143, G.144, N.204, L.207, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:G.13, F:S.138, F:G.141, F:T.143, F:G.144, F:D.177, F:N.204, F:N.204, F:Y.222, F:N.226 pi-Cation interactions: F:Y.222 GDP.12: 13 residues within 4Å: Chain I: 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 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:Q.11, I:Q.11, I:C.12, I:Q.15, I:S.138, I:G.141, I:T.143, I:T.143, I:G.144, I:D.177, I:N.204, I:N.204, I:N.226, I:N.226 pi-Cation interactions: I:Y.222 GDP.15: 17 residues within 4Å: Chain H: L.248, E.254 Chain K: G.10, Q.11, C.12, D.67, 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 K Hydrogen bonds: K:Q.11, K:Q.11, K:C.12, K:N.99, K:S.138, K:G.141, K:T.143, K:T.143, K:T.143, K:G.144, K:D.177, K:E.181, K:N.204, K:N.204, K:N.226, K:N.226 GDP.18: 14 residues within 4Å: Chain J: E.254 Chain M: G.10, Q.11, C.12, D.67, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:Q.11, M:C.12, M:S.138, M:G.141, M:T.143, M:T.143, M:G.144, M:D.177, M:N.204, M:Y.222, M:N.226

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: ACEHJL
Tubulin beta chain: BDFIKM
Protofilament ribbon protein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
D

E
E

H
F

J
G

L
H

B
B

D
I

F
J

I
K

K
L

M
M

G
A

Tubulin alpha chain

Tubulin beta chain

Protofilament ribbon protein

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