SMTL ID : 4yzi.1

Crystal structure of blue-shifted channelrhodopsin mutant (T198G/G202A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 14 residues within 4Å: Chain A: W.125, C.129, G.160, A.164, F.179, G.182, L.183, W.224, F.227, P.228, F.231, D.254, S.257, K.258 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.125, A:W.125, A:A.164, A:F.179, A:F.179, A:L.183, A:W.224, A:F.227, A:F.227, A:F.227, A:F.227, A:F.227, A:P.228, A:F.231, A:K.258 RET.8: 14 residues within 4Å: Chain B: W.125, C.129, G.160, A.164, F.179, G.182, L.183, W.224, F.227, P.228, F.231, D.254, S.257, K.258 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.125, B:W.125, B:A.164, B:F.179, B:F.179, B:L.183, B:W.224, B:F.227, B:F.227, B:F.227, B:F.227, B:F.227, B:P.228, B:F.231, B:K.258

10 x OLA: OLEIC ACID(Non-covalent)

OLA.2: 6 residues within 4Å: Chain A: G.152, S.156, C.184, Y.185, Y.188 Chain B: W.82 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.82, A:Y.185, A:Y.185, A:Y.185, A:Y.188 Hydrogen bonds: A:G.152 OLA.3: 10 residues within 4Å: Chain A: I.97, H.101, D.104, E.105, P.106, A.107, W.119, L.120, A.123 Chain B: T.166 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.97, A:H.101, A:A.107, A:L.120, A:A.123, B:T.166 Hydrogen bonds: A:E.105 Salt bridges: A:H.101 OLA.4: 4 residues within 4Å: Chain A: I.177, F.178, M.181 Chain B: I.93 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.93, A:I.177, A:F.178 OLA.5: 7 residues within 4Å: Chain A: G.172, R.175, V.176, F.179, I.232, G.237, F.238 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.179, A:I.232, A:F.238 Hydrogen bonds: A:G.172, A:G.237 Salt bridges: A:R.175 OLA.6: 4 residues within 4Å: Chain A: E.49, G.245, G.249, I.252 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.252 OLA.9: 6 residues within 4Å: Chain A: W.82 Chain B: G.152, S.156, C.184, Y.185, Y.188 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.185, B:Y.185, B:Y.185, B:Y.188, A:W.82 Hydrogen bonds: B:G.152 OLA.10: 10 residues within 4Å: Chain A: T.166 Chain B: I.97, H.101, D.104, E.105, P.106, A.107, W.119, L.120, A.123 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.97, B:H.101, B:A.107, B:L.120, B:A.123, A:T.166 Hydrogen bonds: B:E.105 Salt bridges: B:H.101 OLA.11: 4 residues within 4Å: Chain A: I.93 Chain B: I.177, F.178, M.181 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.177, B:F.178, A:I.93 OLA.12: 7 residues within 4Å: Chain B: G.172, R.175, V.176, F.179, I.232, G.237, F.238 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.179, B:I.232, B:F.238 Hydrogen bonds: B:G.172, B:G.237 Salt bridges: B:R.175 OLA.13: 4 residues within 4Å: Chain B: E.49, G.245, G.249, I.252 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.252

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: D.2, H.6, H.9, D.104 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.2, A:H.6, A:H.9, A:D.104 ZN.14: 4 residues within 4Å: Chain B: D.2, H.6, H.9, D.104 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.2, B:H.6, B:H.9, B:D.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, H.E. et al., Atomistic design of microbial opsin-based blue-shifted optogenetics tools. Nat Commun (2015)

Release Date

2015-05-27

Peptides

Sensory opsin A,Archaeal-type opsin 2: 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,Archaeal-type opsin 2