SMTL ID : 4cas.1

Serial femtosecond crystallography structure of a photosynthetic reaction center

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: Y.76, K.77, N.78, V.79, K.80, V.81, L.82, F.90, M.94, I.97, T.98, S.102, C.107, C.110, H.111, Y.124, A.127, R.128 Ligands: HEC.2 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:Y.76, A:V.79, A:F.90, A:F.90, A:M.94, A:I.97, A:R.128 Hydrogen bonds: A:K.77, A:N.78, A:K.80, A:V.81, A:L.82 Salt bridges: A:R.128 pi-Stacking: A:Y.124 Metal complexes: A:H.111 HEC.2: 24 residues within 4Å: Chain A: I.97, V.101, Y.109, Y.122, P.123, V.126, M.130, L.131, M.133, T.134, T.151, C.152, C.155, H.156, P.160, L.161, P.162, V.165, L.309, R.313, P.321, C.328 Ligands: HEC.1, HEC.4 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:I.97, A:V.101, A:V.126, A:M.130, A:L.131, A:L.161, A:V.165, A:L.309, A:P.321, A:P.321 Hydrogen bonds: A:Y.109 Salt bridges: A:R.313, A:R.313 Metal complexes: A:H.156 HEC.3: 24 residues within 4Å: Chain A: V.221, R.222, V.223, V.224, T.249, M.253, I.256, S.257, T.262, N.263, C.264, F.266, C.267, H.268, F.273, E.274, R.284, A.287, W.288, R.292 Chain B: Y.163, L.166 Chain C: I.190 Ligands: HEC.4 21 PLIP interactions: 18 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: A:V.221, A:T.249, A:M.253, A:I.256, A:T.262, A:F.266, A:F.273, A:F.273, A:F.273, A:F.273, A:R.284, A:A.287, C:I.190, B:Y.163, B:L.166 Hydrogen bonds: A:V.223, A:V.224 Salt bridges: A:R.222, A:R.292 pi-Cation interactions: A:R.284 Metal complexes: A:H.268 HEC.4: 22 residues within 4Å: Chain A: H.144, V.145, T.148, G.149, V.150, I.256, L.260, Q.283, I.286, A.287, I.291, M.293, V.294, D.324, C.325, C.328, H.329, T.333, K.334, P.335 Ligands: HEC.2, HEC.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.145, A:V.150, A:I.256, A:L.260, A:Q.283, A:I.286, A:A.287, A:I.291, A:K.334, A:P.335 Hydrogen bonds: A:Q.283 Salt bridges: A:K.334, A:K.334 pi-Stacking: A:H.144 Metal complexes: A:H.144, A:H.329

1 x DGA: DIACYL GLYCEROL(Covalent)

DGA.5: 9 residues within 4Å: Chain A: C.21, F.22 Chain B: S.179, W.263, W.266 Chain C: F.89 Ligands: BCL.6, MPG.11, NS5.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.263, B:W.266, C:F.89

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.6: 23 residues within 4Å: Chain B: H.169, M.175, V.178, S.179, F.182, V.183, M.186 Chain C: M.121, F.155, V.156, I.159, I.178, W.179, H.181, I.182, W.184, L.185 Ligands: DGA.5, BCL.7, BCL.13, BPB.14, NS5.16, MPG.18 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:F.155, C:V.156, C:I.159, C:I.178, C:I.182, C:W.184, C:L.185, C:L.185, B:V.178, B:F.182 Metal complexes: C:H.181 pi-Stacking: B:F.182 BCL.7: 31 residues within 4Å: Chain B: F.98, F.122, P.125, I.126, M.128, F.129, L.132, V.158, N.159, F.161, Y.163, W.168, H.169, G.173, H.174, S.177, V.178, L.181, F.182, I.241, F.242, G.245, T.249 Chain C: L.185, Y.196, Y.209 Ligands: BCL.6, BCL.8, BPB.9, BCL.13, MQ7.15 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.98, B:F.122, B:P.125, B:F.161, B:Y.163, B:W.168, B:W.168, B:V.178, B:L.181, B:F.182, B:I.241, B:F.242, B:F.242 Hydrogen bonds: B:S.177, B:T.249 pi-Stacking: B:W.168 Metal complexes: B:H.174 BCL.8: 20 residues within 4Å: Chain B: I.50, F.129, L.132, F.147, I.151, H.154, L.155, V.158 Chain C: Y.196, G.202, I.205, G.206, Y.209, G.210, L.213 Ligands: BCL.7, BPB.9, BCL.13, MQ7.15, OTP.17 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain B, Hydrophobic interactions: C:Y.196, C:I.205, C:I.205, C:Y.209, C:L.213, B:I.50, B:F.129, B:L.132, B:L.132, B:F.147, B:L.155, B:V.158 pi-Stacking: C:Y.209, B:H.154 Metal complexes: B:H.154 BCL.13: 31 residues within 4Å: Chain B: V.158, H.169, F.182 Chain C: G.63, I.67, I.70, M.121, L.125, F.149, A.152, F.155, V.156, I.159, W.184, L.185, T.186, F.188, F.195, Y.196, H.201, S.204, I.205, A.208, Y.209, M.276, A.279, I.283 Ligands: BCL.6, BCL.7, BCL.8, BPB.14 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:I.67, C:I.70, C:L.125, C:F.149, C:A.152, C:F.155, C:V.156, C:W.184, C:L.185, C:F.188, C:F.195, C:Y.196, C:Y.196, C:I.205, C:A.208 Hydrogen bonds: C:S.204 Metal complexes: C:H.201

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.9: 26 residues within 4Å: Chain B: I.43, G.46, I.50, I.90, C.93, A.94, A.97, W.101, E.105, V.118, A.121, F.122, P.125, Y.149, G.150, I.151, H.154, A.238, F.242 Chain C: Y.209, L.213, W.251, I.255 Ligands: BCL.7, BCL.8, MQ7.15 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.43, B:I.50, B:I.90, B:A.97, B:A.121, B:F.122, B:F.122, B:F.122, B:P.125, B:Y.149, B:Y.149, B:F.242, B:F.242, C:Y.209 BPB.14: 21 residues within 4Å: Chain B: F.182, M.186, L.190, F.217, V.220, V.221 Chain C: F.60, S.64, I.67, S.124, L.125, W.128, V.132, I.145, N.148, F.149, S.272, M.276 Ligands: BCL.6, BCL.13, NS5.16 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.182, B:M.186, B:L.190, C:F.60, C:I.67, C:I.67, C:W.128, C:I.145, C:N.148, C:F.149, C:F.149 pi-Stacking: C:F.149

3 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.10: 8 residues within 4Å: Chain B: W.116, H.117, L.120, R.232, S.239 Chain C: A.2, T.6, I.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.120, B:L.120, B:R.232, C:I.7 Hydrogen bonds: C:A.2 MPG.11: 14 residues within 4Å: Chain B: F.180, V.183, L.190, H.191, L.194, F.217, S.224, I.225, G.226, I.230, F.236, L.237 Ligands: DGA.5, MPG.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.180, B:V.183, B:F.236, B:L.237 Hydrogen bonds: B:H.191, B:I.225, B:G.226 MPG.18: 4 residues within 4Å: Chain C: G.31, G.48 Ligands: BCL.6, MPG.11 No protein-ligand interaction detected (PLIP)

1 x FE2: FE (II) ION(Non-covalent)

FE2.12: 5 residues within 4Å: Chain B: H.191, H.231 Chain C: H.218, E.233, H.265 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.218, C:E.233, C:E.233, C:H.265, B:H.191

1 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.15: 23 residues within 4Å: Chain B: Y.30, I.40, W.101, R.104 Chain C: A.217, H.218, T.221, V.244, A.247, A.248, W.251, I.255, F.257, N.258, A.259, T.260, V.264, W.267, F.271 Ligands: BCL.7, BCL.8, BPB.9, OTP.17 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.217, C:A.247, C:A.248, C:W.251, C:I.255, C:F.257, C:F.257, C:V.264, C:W.267, C:W.267, C:F.271, B:Y.30, B:Y.30, B:W.101 Hydrogen bonds: C:H.218, C:A.259 pi-Stacking: C:W.251

1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)

NS5.16: 19 residues within 4Å: Chain C: I.67, L.71, M.74, F.89, L.115, G.118, L.119, T.122, V.156, G.160, C.161, V.174, F.176, G.177, I.178, H.181 Ligands: DGA.5, BCL.6, BPB.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.67, C:F.89, C:L.115, C:V.174, C:I.178

1 x OTP: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

OTP.17: 14 residues within 4Å: Chain B: F.63, L.152 Chain C: P.199, G.202, F.203, F.207, W.296, C.297, A.302 Chain D: Q.14, W.25, L.29 Ligands: BCL.8, MQ7.15 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:F.207, C:A.302, B:F.63, D:Q.14, D:W.25, D:L.29

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.19: 7 residues within 4Å: Chain C: W.24, Y.51, G.53, A.54, S.55, I.130, S.134 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.24, C:Y.51, C:A.54, C:S.55, C:S.55, C:S.134, C:S.134 PO4.20: 3 residues within 4Å: Chain B: N.200 Chain C: H.144, R.266 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.266 Salt bridges: C:H.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, L.C. et al., Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun (2013)

Release Date

2013-12-25

Peptides

PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT: A
REACTION CENTER PROTEIN L CHAIN: B
REACTION CENTER PROTEIN M CHAIN: C
REACTION CENTER PROTEIN H CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT

REACTION CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

REACTION CENTER PROTEIN H CHAIN

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