SMTL ID : 7c86.1

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.61 No protein-ligand interaction detected (PLIP)

2 x RET: RETINAL(Covalent)

RET.2: 15 residues within 4Å: Chain A: E.162, W.163, T.166, C.167, T.198, G.202, F.217, G.220, L.221, W.262, F.265, P.266, D.292, S.295, K.296 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.163, A:W.163, A:W.163, A:T.198, A:F.217, A:W.262, A:W.262, A:F.265, A:F.265, A:F.265, A:F.265, A:F.265, A:K.296 RET.13: 15 residues within 4Å: Chain B: E.162, W.163, T.166, C.167, T.198, G.202, F.217, G.220, L.221, W.262, F.265, P.266, D.292, S.295, K.296 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.163, B:W.163, B:W.163, B:T.198, B:F.217, B:W.262, B:W.262, B:F.265, B:F.265, B:F.265, B:F.265, B:F.265, B:K.296

18 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.3: 8 residues within 4Å: Chain A: G.210, R.213, V.214, F.217, I.267, I.270, G.275, F.276 Ligand excluded by PLIP OLC.4: 4 residues within 4Å: Chain A: I.215, F.216, M.219 Chain B: I.131 Ligand excluded by PLIP OLC.5: 3 residues within 4Å: Chain A: A.86, L.89, A.90 Ligand excluded by PLIP OLC.6: 8 residues within 4Å: Chain A: K.186, R.187, G.190, C.222, Y.223, Y.226 Chain B: W.120 Ligands: OLC.21 Ligand excluded by PLIP OLC.7: 12 residues within 4Å: Chain A: W.201, T.204, Y.211, V.212, F.216 Chain B: I.135, H.139, D.142, E.143, P.144, A.145, L.158 Ligand excluded by PLIP OLC.8: 3 residues within 4Å: Chain A: Y.239, A.255 Ligands: OLC.11 Ligand excluded by PLIP OLC.9: 1 residues within 4Å: Chain A: F.229 Ligand excluded by PLIP OLC.10: 3 residues within 4Å: Chain A: I.131 Chain B: Y.223 Ligands: OLC.17 Ligand excluded by PLIP OLC.11: 2 residues within 4Å: Chain A: W.256 Ligands: OLC.8 Ligand excluded by PLIP OLC.14: 8 residues within 4Å: Chain B: G.210, R.213, V.214, F.217, I.267, I.270, G.275, F.276 Ligand excluded by PLIP OLC.15: 4 residues within 4Å: Chain A: I.131 Chain B: I.215, F.216, M.219 Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain B: A.86, L.89, A.90 Ligand excluded by PLIP OLC.17: 8 residues within 4Å: Chain A: W.120 Chain B: K.186, R.187, G.190, C.222, Y.223, Y.226 Ligands: OLC.10 Ligand excluded by PLIP OLC.18: 12 residues within 4Å: Chain A: I.135, H.139, D.142, E.143, P.144, A.145, L.158 Chain B: W.201, T.204, Y.211, V.212, F.216 Ligand excluded by PLIP OLC.19: 3 residues within 4Å: Chain B: Y.239, A.255 Ligands: OLC.22 Ligand excluded by PLIP OLC.20: 1 residues within 4Å: Chain B: F.229 Ligand excluded by PLIP OLC.21: 3 residues within 4Å: Chain A: Y.223 Chain B: I.131 Ligands: OLC.6 Ligand excluded by PLIP OLC.22: 2 residues within 4Å: Chain B: W.256 Ligands: OLC.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oda, K. et al., Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife (2021)

Release Date

2021-04-07

Peptides

Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Sensory opsin A,Channelrhodopsin (ChR) chimera between ChR1 & ChR2

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