SMTL ID : 7voy.1

Rba sphaeroides PufX-KO RC-LH1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-17-17-1-1-1-mer

Ligands

38 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 13 residues within 4Å: Chain 0: I.31 Chain A: A.28, H.32, W.43 Chain B: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.2, BCL.28 8 PLIP interactions: 3 interactions with chain B, 1 interactions with chain 0, 4 interactions with chain A, Hydrophobic interactions: B:A.38, B:V.42, B:W.45, 0:I.31, A:A.28, A:W.43, A:W.43, A:W.43 BCL.2: 14 residues within 4Å: Chain A: L.24, A.28, I.31, H.32, L.35, Y.41 Chain B: F.31, A.35, H.39, W.48, F.49 Chain C: W.43 Ligands: BCL.1, BCL.3 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:I.31, A:Y.41, B:F.31, B:A.35, B:W.48, B:W.48, B:W.48 Metal complexes: B:H.39 BCL.3: 12 residues within 4Å: Chain A: I.31 Chain C: H.32, W.43 Chain D: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.2, BCL.4 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: C:W.43, C:W.43, C:W.43, D:A.38, D:W.45, A:I.31 pi-Stacking: C:H.32 BCL.4: 15 residues within 4Å: Chain C: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain D: F.31, A.35, H.39, W.48, F.49 Chain E: W.43 Ligands: BCL.3, BCL.5 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D, Hydrophobic interactions: C:I.31, C:Y.41, D:F.31, D:A.35, D:W.48, D:W.48, D:W.48 Metal complexes: D:H.39 BCL.5: 12 residues within 4Å: Chain E: F.25, A.28, H.32, L.35, W.43 Chain F: F.31, V.34, A.35, A.38, H.39 Ligands: BCL.4, BCL.6 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E, Hydrophobic interactions: F:A.38, E:L.35, E:W.43, E:W.43, E:W.43, E:W.43 BCL.6: 15 residues within 4Å: Chain E: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain F: F.31, A.35, H.39, W.48, F.49 Chain G: W.43 Ligands: BCL.5, BCL.7 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain E, Hydrophobic interactions: F:F.31, F:A.35, F:W.48, F:W.48, F:W.48, E:I.31, E:L.35, E:Y.41 Metal complexes: F:H.39 BCL.7: 13 residues within 4Å: Chain E: I.31 Chain G: A.28, H.32, L.35, W.43 Chain H: F.31, V.34, A.35, A.38, H.39, V.42 Ligands: BCL.6, BCL.8 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E, 3 interactions with chain G, Hydrophobic interactions: H:A.38, E:I.31, G:L.35, G:W.43, G:W.43 BCL.8: 15 residues within 4Å: Chain G: L.24, A.28, I.31, H.32, L.35, Y.41 Chain H: F.31, A.35, H.39, W.48, F.49 Chain I: W.43, L.44 Ligands: BCL.7, BCL.9 10 PLIP interactions: 1 interactions with chain I, 3 interactions with chain G, 6 interactions with chain H, Hydrophobic interactions: I:L.44, G:I.31, G:L.35, G:Y.41, H:F.31, H:A.35, H:W.48, H:W.48, H:W.48 Metal complexes: H:H.39 BCL.9: 11 residues within 4Å: Chain I: A.28, H.32, W.43 Chain J: F.31, V.34, A.35, A.38, H.39, V.42 Ligands: BCL.8, BCL.10 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I, Hydrophobic interactions: J:A.38, J:V.42, I:W.43, I:W.43 BCL.10: 15 residues within 4Å: Chain I: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain J: F.31, A.35, H.39, W.48, F.49 Chain K: W.43 Ligands: BCL.9, BCL.11 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I, Hydrophobic interactions: J:F.31, J:A.35, J:W.48, J:W.48, J:W.48, I:I.31, I:Y.41 Metal complexes: J:H.39 BCL.11: 15 residues within 4Å: Chain I: I.31 Chain K: L.24, F.25, A.28, H.32, W.43 Chain L: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.10, BCL.12 6 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K, 1 interactions with chain I, Hydrophobic interactions: L:A.38, L:W.45, K:W.43, K:W.43, K:W.43, I:I.31 BCL.12: 15 residues within 4Å: Chain K: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain L: F.31, A.35, H.39, W.48, F.49 Chain M: W.43 Ligands: BCL.11, BCL.13 10 PLIP interactions: 6 interactions with chain L, 4 interactions with chain K, Hydrophobic interactions: L:F.31, L:A.35, L:W.48, L:W.48, L:W.48, K:I.31, K:L.35, K:L.35, K:Y.41 Metal complexes: L:H.39 BCL.13: 13 residues within 4Å: Chain K: I.31 Chain L: F.49 Chain M: A.28, H.32, W.43 Chain N: F.31, V.34, A.35, A.38, H.39, W.45 Ligands: BCL.12, BCL.14 7 PLIP interactions: 2 interactions with chain N, 1 interactions with chain L, 2 interactions with chain K, 2 interactions with chain M, Hydrophobic interactions: N:A.38, N:W.45, L:F.49, K:I.31, K:I.31, M:W.43, M:W.43 BCL.14: 14 residues within 4Å: Chain M: L.24, A.28, I.31, H.32, L.35, Y.41 Chain N: F.31, A.35, H.39, W.48, F.49 Chain O: W.43 Ligands: BCL.13, BCL.15 10 PLIP interactions: 4 interactions with chain M, 6 interactions with chain N, Hydrophobic interactions: M:I.31, M:L.35, M:L.35, M:Y.41, N:F.31, N:A.35, N:W.48, N:W.48, N:W.48 Metal complexes: N:H.39 BCL.15: 13 residues within 4Å: Chain M: I.31 Chain O: A.28, H.32, L.35, W.43 Chain P: F.31, V.34, A.35, A.38, H.39, W.45 Ligands: BCL.14, BCL.16 9 PLIP interactions: 2 interactions with chain M, 5 interactions with chain O, 2 interactions with chain P, Hydrophobic interactions: M:I.31, M:I.31, O:L.35, O:W.43, O:W.43, O:W.43, P:A.38, P:W.45 Metal complexes: O:H.32 BCL.16: 14 residues within 4Å: Chain O: L.24, A.28, I.31, H.32, L.35, Y.41 Chain P: F.31, A.35, H.39, W.48, F.49 Chain Q: W.43 Ligands: BCL.15, BCL.17 10 PLIP interactions: 4 interactions with chain O, 6 interactions with chain P, Hydrophobic interactions: O:I.31, O:L.35, O:L.35, O:Y.41, P:F.31, P:A.35, P:W.48, P:W.48, P:W.48 Metal complexes: P:H.39 BCL.17: 14 residues within 4Å: Chain O: I.31 Chain P: F.49 Chain Q: A.28, H.32, W.43 Chain R: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.16, BCL.18 8 PLIP interactions: 3 interactions with chain R, 2 interactions with chain O, 2 interactions with chain Q, 1 interactions with chain P, Hydrophobic interactions: R:A.38, R:V.42, R:W.45, O:I.31, O:I.31, Q:W.43, Q:W.43, P:F.49 BCL.18: 15 residues within 4Å: Chain Q: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain R: F.31, A.35, H.39, W.48, F.49 Chain S: W.43 Ligands: BCL.17, BCL.19 10 PLIP interactions: 4 interactions with chain Q, 6 interactions with chain R, Hydrophobic interactions: Q:I.31, Q:L.35, Q:Y.41, R:F.31, R:A.35, R:W.48, R:W.48, R:W.48 Hydrogen bonds: Q:H.32 Metal complexes: R:H.39 BCL.19: 12 residues within 4Å: Chain Q: I.31 Chain S: H.32, W.43 Chain T: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.18, BCL.20 8 PLIP interactions: 2 interactions with chain T, 2 interactions with chain Q, 4 interactions with chain S, Hydrophobic interactions: T:A.38, T:W.45, Q:I.31, Q:I.31, S:W.43, S:W.43, S:W.43, S:W.43 BCL.20: 14 residues within 4Å: Chain S: L.24, A.28, I.31, H.32, L.35, Y.41 Chain T: F.31, A.35, H.39, W.48, F.49 Chain U: W.43 Ligands: BCL.19, BCL.21 10 PLIP interactions: 4 interactions with chain S, 6 interactions with chain T, Hydrophobic interactions: S:I.31, S:L.35, S:Y.41, T:F.31, T:A.35, T:W.48, T:W.48, T:W.48 Hydrogen bonds: S:H.32 Metal complexes: T:H.39 BCL.21: 13 residues within 4Å: Chain T: F.49 Chain U: A.28, H.32, W.43 Chain V: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.20, BCL.22 6 PLIP interactions: 3 interactions with chain U, 2 interactions with chain V, 1 interactions with chain T, Hydrophobic interactions: U:W.43, U:W.43, U:W.43, V:A.38, V:W.45, T:F.49 BCL.22: 15 residues within 4Å: Chain U: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain V: F.31, A.35, H.39, W.48, F.49 Chain W: W.43 Ligands: BCL.21, BCL.23 9 PLIP interactions: 6 interactions with chain V, 3 interactions with chain U, Hydrophobic interactions: V:F.31, V:A.35, V:W.48, V:W.48, V:W.48, U:I.31, U:L.35, U:Y.41 Metal complexes: V:H.39 BCL.23: 14 residues within 4Å: Chain U: I.31 Chain W: A.28, H.32, L.35, W.43 Chain X: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.22, BCL.24 7 PLIP interactions: 4 interactions with chain W, 3 interactions with chain X, Hydrophobic interactions: W:L.35, W:W.43, W:W.43, X:A.38, X:V.42, X:W.45 Metal complexes: W:H.32 BCL.24: 12 residues within 4Å: Chain 6: W.43 Chain W: A.28, I.31, H.32, L.35 Chain X: F.31, A.35, H.39, W.48, F.49 Ligands: BCL.23, BCL.33 8 PLIP interactions: 6 interactions with chain X, 2 interactions with chain W, Hydrophobic interactions: X:F.31, X:A.35, X:W.48, X:W.48, X:W.48, W:I.31, W:L.35 Metal complexes: X:H.39 BCL.25: 11 residues within 4Å: Chain Y: A.28, H.32, W.43 Chain Z: F.31, V.34, A.35, A.38, H.39, V.42 Ligands: BCL.26, BCL.30 5 PLIP interactions: 3 interactions with chain Z, 2 interactions with chain Y, Hydrophobic interactions: Z:A.38, Z:V.42, Z:V.42, Y:W.43, Y:W.43 BCL.26: 15 residues within 4Å: Chain 0: W.43 Chain Y: L.24, L.27, A.28, I.31, H.32, L.35, Y.41 Chain Z: F.31, A.35, H.39, W.48, F.49 Ligands: BCL.25, BCL.27 9 PLIP interactions: 3 interactions with chain Y, 6 interactions with chain Z, Hydrophobic interactions: Y:I.31, Y:I.31, Y:Y.41, Z:F.31, Z:A.35, Z:W.48, Z:W.48, Z:W.48 Metal complexes: Z:H.39 BCL.27: 12 residues within 4Å: Chain 0: A.28, H.32, W.43 Chain 1: F.31, V.34, A.35, A.38, H.39, V.42 Chain Y: I.31 Ligands: BCL.26, BCL.28 7 PLIP interactions: 4 interactions with chain 0, 1 interactions with chain Y, 2 interactions with chain 1, Hydrophobic interactions: 0:W.43, 0:W.43, 0:W.43, 0:W.43, Y:I.31, 1:A.38, 1:V.42 BCL.28: 14 residues within 4Å: Chain 0: L.24, A.28, I.31, H.32, L.35, Y.41 Chain 1: F.31, A.35, H.39, W.48, F.49 Chain A: W.43 Ligands: BCL.1, BCL.27 9 PLIP interactions: 6 interactions with chain 1, 3 interactions with chain 0, Hydrophobic interactions: 1:F.31, 1:A.35, 1:W.48, 1:W.48, 1:W.48, 0:I.31, 0:L.35, 0:Y.41 Metal complexes: 1:H.39 BCL.29: 10 residues within 4Å: Chain 2: A.28, H.32, W.43 Chain 3: F.31, V.34, A.35, A.38, H.39 Ligands: BCL.30, BCL.32 5 PLIP interactions: 4 interactions with chain 2, 1 interactions with chain 3, Hydrophobic interactions: 2:W.43, 2:W.43, 2:W.43, 2:W.43, 3:A.38 BCL.30: 15 residues within 4Å: Chain 2: L.24, A.28, I.31, H.32, L.35, Y.41 Chain 3: F.31, A.35, H.39, W.48, F.49 Chain Y: W.43, L.44 Ligands: BCL.25, BCL.29 9 PLIP interactions: 2 interactions with chain 2, 6 interactions with chain 3, 1 interactions with chain Y, Hydrophobic interactions: 2:I.31, 2:Y.41, 3:F.31, 3:A.35, 3:W.48, 3:W.48, 3:W.48, Y:L.44 Metal complexes: 3:H.39 BCL.31: 10 residues within 4Å: Chain 4: A.28, H.32, W.43 Chain 5: F.31, A.38, H.39, V.42, W.45 Ligands: BCL.32, BCL.34 4 PLIP interactions: 2 interactions with chain 5, 2 interactions with chain 4, Hydrophobic interactions: 5:A.38, 5:W.45, 4:W.43, 4:W.43 BCL.32: 14 residues within 4Å: Chain 2: W.43 Chain 4: L.24, A.28, I.31, H.32, L.35, Y.41 Chain 5: F.31, A.35, H.39, W.48, F.49 Ligands: BCL.29, BCL.31 9 PLIP interactions: 3 interactions with chain 4, 6 interactions with chain 5, Hydrophobic interactions: 4:I.31, 4:L.35, 4:Y.41, 5:F.31, 5:A.35, 5:W.48, 5:W.48, 5:W.48 Metal complexes: 5:H.39 BCL.33: 12 residues within 4Å: Chain 6: A.28, H.32, W.43 Chain 7: F.31, V.34, A.35, A.38, H.39, V.42, W.45 Ligands: BCL.24, BCL.34 7 PLIP interactions: 4 interactions with chain 6, 3 interactions with chain 7, Hydrophobic interactions: 6:W.43, 6:W.43, 6:W.43, 6:W.43, 7:A.38, 7:V.42, 7:W.45 BCL.34: 13 residues within 4Å: Chain 4: W.43 Chain 6: L.24, A.28, I.31, H.32, Y.41 Chain 7: F.31, A.35, H.39, W.48, F.49 Ligands: BCL.31, BCL.33 8 PLIP interactions: 6 interactions with chain 7, 2 interactions with chain 6, Hydrophobic interactions: 7:F.31, 7:A.35, 7:W.48, 7:W.48, 7:W.48, 6:I.31, 6:Y.41 Metal complexes: 7:H.39 BCL.35: 17 residues within 4Å: Chain 8: L.132, L.155, T.161, Y.163, F.168, H.169, H.174, A.177, I.178, F.181, F.182, V.242, S.245 Chain 9: L.210, Y.211 Ligands: BCL.40, BCL.41 10 PLIP interactions: 8 interactions with chain 8, 2 interactions with chain 9, Hydrophobic interactions: 8:T.161, 8:Y.163, 8:F.168, 8:F.168, 8:A.177, 8:I.178, 9:L.210 Hydrogen bonds: 8:S.245, 9:Y.211 Metal complexes: 8:H.174 BCL.38: 9 residues within 4Å: Chain 8: Y.129, F.147, Y.149, L.155 Chain 9: G.204, I.207, A.208, Y.211 Ligands: BPH.36 7 PLIP interactions: 3 interactions with chain 9, 4 interactions with chain 8, Hydrophobic interactions: 9:I.207, 9:A.208, 9:Y.211, 8:Y.129, 8:F.147, 8:Y.149, 8:L.155 BCL.40: 12 residues within 4Å: Chain 8: H.169, M.175, I.178, F.182 Chain 9: W.158, H.183, L.184, T.187 Ligands: BCL.35, BCL.41, BPH.42, SPN.44 4 PLIP interactions: 1 interactions with chain 9, 3 interactions with chain 8, Hydrophobic interactions: 9:L.184, 8:H.169, 8:I.178, 8:F.182 BCL.41: 16 residues within 4Å: Chain 9: L.157, T.187, N.188, F.190, S.191, L.197, F.198, H.203, S.206, I.207, V.277, T.278, G.281, I.285 Ligands: BCL.35, BCL.40 4 PLIP interactions: 4 interactions with chain 9, Hydrophobic interactions: 9:F.190, 9:F.198, 9:V.277 Salt bridges: 9:H.203

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.36: 10 residues within 4Å: Chain 8: T.39, A.43, F.98, W.101, F.122, A.125 Chain 9: L.215, M.219, M.257 Ligands: BCL.38 5 PLIP interactions: 4 interactions with chain 8, 1 interactions with chain 9 Hydrophobic interactions: 8:F.98, 8:W.101, 8:F.122, 8:A.125, 9:L.215 BPH.42: 13 residues within 4Å: Chain 8: F.182, A.185, L.186, A.189, L.190 Chain 9: W.130, A.150, F.151, A.154, A.274, V.277, T.278 Ligands: BCL.40 10 PLIP interactions: 7 interactions with chain 9, 3 interactions with chain 8 Hydrophobic interactions: 9:W.130, 9:A.150, 9:A.154, 9:A.274, 9:V.277, 9:V.277, 9:T.278, 8:F.182, 8:L.186, 8:A.189

2 x U10: UBIQUINONE-10(Non-covalent)

U10.37: 9 residues within 4Å: Chain 8: L.190, H.191, L.194, F.217, S.224, I.225, G.226, T.227, I.230 7 PLIP interactions: 7 interactions with chain 8 Hydrophobic interactions: 8:L.190, 8:I.225, 8:I.230, 8:I.230 Hydrogen bonds: 8:I.225, 8:G.226 pi-Stacking: 8:F.217 U10.43: 9 residues within 4Å: Chain 9: H.220, T.223, A.249, A.250, W.253, A.261, T.262, M.263, I.266 7 PLIP interactions: 7 interactions with chain 9 Hydrophobic interactions: 9:W.253, 9:A.261, 9:I.266 Hydrogen bonds: 9:H.220, 9:T.223, 9:A.261 pi-Stacking: 9:W.253

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

FE2.39: 3 residues within 4Å: Chain 9: M.263, I.266, H.267 No protein-ligand interaction detected (PLIP)

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.44: 20 residues within 4Å: Chain 9: F.68, F.69, I.71, G.72, L.117, S.120, F.121, M.123, F.124, W.158, M.159, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, I.180 Ligands: BCL.40 13 PLIP interactions: 13 interactions with chain 9 Hydrophobic interactions: 9:F.68, 9:F.68, 9:F.68, 9:I.71, 9:L.117, 9:F.124, 9:W.158, 9:L.161, 9:W.172, 9:V.176, 9:Y.178, 9:Y.178, 9:I.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, P. et al., Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex. Nat Commun (2022)

Release Date

2022-05-04

Peptides

Light-harvesting protein B-875 alpha chain: ACEGIKMOQSUWY0246
Light-harvesting protein B-875 beta chain: BDFHJLNPRTVXZ1357
Reaction center protein L chain: 8
Reaction center protein M chain: 9
Reaction center protein H chain: a

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
F

G
I

I
K

K
O

M
Q

O
S

Q
U

S
W

U
Y

W
1

Y
7

0
9

2
4

4
6

6
C

B
B

D
E

F
G

H
J

J
N

L
P

N
R

P
T

R
V

T
X

V
Z

X
2

Z
8

1
0

3
t

5
5

7
3

8
L

9
M

a
H

Membrane

We predict this structure to be a membrane protein.
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Light-harvesting protein B-875 alpha chain

Light-harvesting protein B-875 beta chain

Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

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