SMTL ID : 8to2.1

Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-10-11-1-1-1-1-mer

Ligands

24 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 30 residues within 4Å: Chain 1: F.60, I.67, T.75, T.76, F.79 Chain A: I.75, F.76, I.139, Y.144, N.148, K.151, S.152, R.154, D.155, M.156, W.158, F.159, Y.162, I.175, N.178, T.179, L.182, V.185, I.186, A.189, C.190, S.191, A.194, T.195, A.198 Ligand excluded by PLIP CYC.3: 31 residues within 4Å: Chain D: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain I: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.4: 33 residues within 4Å: Chain C: R.2, F.4, Y.33, W.36, F.37, Q.40, Q.41, M.44 Chain E: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.5: 31 residues within 4Å: Chain E: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain F: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Ligand excluded by PLIP CYC.6: 30 residues within 4Å: Chain A: K.533, V.563, I.566, E.569, N.570 Chain G: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.7: 33 residues within 4Å: Chain G: L.61, Y.62, T.66, R.67, Y.73, T.74, T.75, Y.78 Chain H: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Ligand excluded by PLIP CYC.8: 33 residues within 4Å: Chain C: V.10, P.11, S.12, Q.13, R.20, E.21, L.22, T.25 Chain I: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.9: 33 residues within 4Å: Chain 2: R.100 Chain J: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain K: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.10: 32 residues within 4Å: Chain A: Y.447, Y.597, V.598, C.599, R.617, N.621, F.624 Chain K: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.11: 34 residues within 4Å: Chain B: I.11 Chain L: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain M: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.12: 31 residues within 4Å: Chain A: I.456, Q.457, F.458, G.459, I.461, R.553 Chain M: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.13: 33 residues within 4Å: Chain N: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain O: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.14: 32 residues within 4Å: Chain A: I.483, L.484, I.485, H.486, A.490, N.493, V.495 Chain O: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.15: 33 residues within 4Å: Chain R: L.58, F.59, Y.65, N.71, A.72, Q.77, Q.80, C.81, R.83, D.84, Y.85, W.87, Y.88, R.90, L.91, T.107, G.108, M.115, Y.116, L.119, V.121, P.122, G.125, M.126, A.129 Chain W: L.61, Y.62, T.66, R.67, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.16: 33 residues within 4Å: Chain Q: R.2, F.4, Y.33, W.36, F.37, Q.40, Q.41, M.44 Chain S: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.17: 33 residues within 4Å: Chain S: K.53, L.61, Y.62, S.63, T.66, Y.73, T.74, T.75, Y.78 Chain T: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Ligand excluded by PLIP CYC.18: 31 residues within 4Å: Chain A: Y.304, S.307, Q.308, R.310, N.311, D.313 Chain U: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.19: 32 residues within 4Å: Chain U: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain V: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Ligand excluded by PLIP CYC.20: 31 residues within 4Å: Chain Q: P.11, S.12, R.15, L.22, Q.23, N.24, T.25 Chain W: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.21: 34 residues within 4Å: Chain X: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain Y: L.61, Y.62, S.63, T.66, Y.73, T.74, T.75, Y.78 Ligand excluded by PLIP CYC.22: 33 residues within 4Å: Chain A: I.338, N.339, S.340, R.358, V.361, Q.362, F.365, I.431, R.439 Chain Y: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 Ligand excluded by PLIP CYC.23: 34 residues within 4Å: Chain 0: L.61, Y.62, S.63, T.66, Y.73, T.74, T.75, Y.78 Chain Z: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Ligand excluded by PLIP CYC.24: 28 residues within 4Å: Chain 0: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126 Chain A: R.292, Y.298, Y.420, F.424 Ligand excluded by PLIP CYC.25: 36 residues within 4Å: Chain 1: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, Y.88, Y.89, Y.92, R.108, V.109, L.113, T.116, Y.117, L.120, V.122, P.123, P.126, T.127 Chain A: P.14, Q.249, L.251, L.253, Y.257, L.401, A.405, Q.406, E.407, C.408, W.411 Ligand excluded by PLIP

1 x 45D: beta,beta-carotene-4,4'-dione(Non-covalent)

45D.2: 38 residues within 4Å: Chain B: E.34, L.37, A.38, I.40, W.41, A.43, Y.44, M.47, T.52, I.53, A.54, A.55, P.56, A.58, A.59, T.80, M.83, C.84, N.104, L.107, G.108, W.110, Y.111, L.113, G.114, M.117, I.125, P.126, Y.129, I.151, L.154, R.155, E.174, V.176, V.177 Chain L: P.68, G.69, Y.73 28 PLIP interactions: 3 interactions with chain L, 25 interactions with chain B Hydrophobic interactions: L:P.68, L:Y.73, B:E.34, B:L.37, B:L.37, B:L.37, B:A.38, B:I.40, B:I.40, B:W.41, B:Y.44, B:A.54, B:A.55, B:A.58, B:T.80, B:L.107, B:L.107, B:L.107, B:W.110, B:W.110, B:L.113, B:I.125, B:Y.129, B:Y.129, B:I.151, B:L.154, B:V.177 Hydrogen bonds: L:G.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauer, P.V. et al., Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Sci Adv (2024)

Release Date

2024-04-17

Peptides

Phycobiliprotein ApcE: A
Orange carotenoid-binding protein: B
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: CQ
Allophycocyanin alpha chain: DFHJLNTVXZ
Allophycocyanin beta chain: EGIKMOSUWY0
Phycobilisome rod-core linker polypeptide CpcG: P
Allophycocyanin subunit alpha-B: R
Allophycocyanin subunit beta-18: 1
Translation initiation factor IF-2: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Q
c

D
D

F
F

H
H

J
J

L
L

N
N

T
f

V
h

X
j

Z
l

E
E

G
G

I
I

K
K

M
M

O
O

S
e

U
g

W
i

Y
k

0
m

P
P

R
d

1
o

2
p

Phycobiliprotein ApcE

Orange carotenoid-binding protein

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Allophycocyanin alpha chain

Allophycocyanin beta chain

Phycobilisome rod-core linker polypeptide CpcG

Allophycocyanin subunit alpha-B

Allophycocyanin subunit beta-18

Translation initiation factor IF-2

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