SMTL ID : 8hfq.1

Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-18-1-1-1-1-mer

Ligands

54 x CYC: PHYCOCYANOBILIN(Non-covalent)(Covalent)

CYC.1: 27 residues within 4Å: Chain A: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, I.88, Y.90, I.94, Y.110, L.111, I.115, F.122, L.124, W.128, Y.129 Chain F: R.57, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.2: 29 residues within 4Å: Chain B: L.66, N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, S.126, V.127 Chain d: N.55, Q.57, Q.58, A.177, R.178, M.179, P.180, R.181, Y.182 Ligand excluded by PLIP CYC.3: 22 residues within 4Å: Chain A: F.28 Chain B: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Chain G: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.4: 30 residues within 4Å: Chain B: R.57, I.67, Y.74, T.75, S.76, M.79 Chain C: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.5: 28 residues within 4Å: Chain D: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain d: I.6, N.102, Y.103, I.125, S.128, I.129, A.132 Ligand excluded by PLIP CYC.6: 20 residues within 4Å: Chain C: F.28 Chain D: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Chain K: Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.7: 30 residues within 4Å: Chain D: R.57, I.67, Y.74, T.75, S.76, M.79 Chain E: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.8: 28 residues within 4Å: Chain F: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain d: S.12, Q.13, N.14, R.16, V.17, R.163, L.166, R.169 Ligand excluded by PLIP CYC.9: 20 residues within 4Å: Chain E: L.24, F.28 Chain F: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, D.144, I.148, T.149, R.150, G.151, C.153 Chain I: R.32, Q.33, D.145, D.148 Ligand excluded by PLIP CYC.10: 28 residues within 4Å: Chain G: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.91, I.94, Y.110, I.115, I.118, F.122, L.124, W.128, Y.129 Chain L: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.11: 27 residues within 4Å: Chain H: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain a: S.247, G.250, Y.251, V.254, R.255 Ligand excluded by PLIP CYC.12: 21 residues within 4Å: Chain A: Q.33, D.145, E.149 Chain G: L.24, F.28 Chain H: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.13: 26 residues within 4Å: Chain H: R.57, I.67, Y.74, T.75, M.79 Chain I: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.14: 28 residues within 4Å: Chain J: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, P.123, S.126, V.127 Chain a: K.237, F.265, L.268, N.269, L.272, Q.273, N.276 Ligand excluded by PLIP CYC.15: 23 residues within 4Å: Chain E: R.32, Q.33, D.145, D.148, E.149 Chain I: L.24, F.28 Chain J: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.16: 30 residues within 4Å: Chain J: R.57, I.67, Y.74, T.75, S.76, M.79 Chain K: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.17: 25 residues within 4Å: Chain L: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, P.123, S.126, V.127 Chain a: L.226 Chain d: A.67, S.70, Q.71, K.73, N.74 Ligand excluded by PLIP CYC.18: 22 residues within 4Å: Chain C: R.32, Q.33, D.145, E.149 Chain K: L.24, F.28 Chain L: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.19: 28 residues within 4Å: Chain M: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain R: R.57, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.20: 27 residues within 4Å: Chain N: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, S.126, V.127 Chain a: F.91, Q.92, T.93, E.111, I.115, L.118 Ligand excluded by PLIP CYC.21: 21 residues within 4Å: Chain M: L.24, F.28 Chain N: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Chain S: Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.22: 29 residues within 4Å: Chain N: R.57, I.67, Y.74, T.75, S.76, M.79 Chain O: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.23: 28 residues within 4Å: Chain P: L.59, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, P.123, S.126, V.127 Chain a: A.2, I.3, T.4, T.5, F.153, N.154, N.155, D.159 Ligand excluded by PLIP CYC.24: 22 residues within 4Å: Chain O: F.28 Chain P: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Chain W: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.25: 27 residues within 4Å: Chain P: R.57, I.67, Y.74, T.75, M.79 Chain Q: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.26: 25 residues within 4Å: Chain R: L.59, N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, L.120, S.126, V.127 Chain a: R.41, N.46, D.47, Y.48, Y.174, A.175, S.177 Ligand excluded by PLIP CYC.27: 21 residues within 4Å: Chain Q: F.28 Chain R: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Chain U: Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.28: 28 residues within 4Å: Chain S: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, I.115, F.122, L.124, W.128, Y.129 Chain X: R.57, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.29: 27 residues within 4Å: Chain T: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, S.126, V.127 Chain a: G.57, S.60, L.61, T.63, N.64 Chain b: L.211, G.213 Ligand excluded by PLIP CYC.30: 22 residues within 4Å: Chain M: R.32, Q.33, D.145, E.149 Chain S: S.21, L.24, F.28 Chain T: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.31: 28 residues within 4Å: Chain T: R.57, I.67, Y.74, T.75, S.76, M.79 Chain U: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.32: 26 residues within 4Å: Chain V: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: A.231, R.238, V.239, R.240 Ligand excluded by PLIP CYC.33: 20 residues within 4Å: Chain Q: R.32, Q.33, D.145, E.149 Chain U: F.28 Chain V: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.34: 27 residues within 4Å: Chain V: R.57, I.67, Y.74, T.75, S.76, M.79 Chain W: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, Y.90, Y.91, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.35: 25 residues within 4Å: Chain X: L.59, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, P.123, S.126, V.127 Chain b: R.219, Y.250, S.254, Q.258, N.261 Ligand excluded by PLIP CYC.36: 21 residues within 4Å: Chain O: R.32, Q.33, D.145, D.148 Chain W: F.28 Chain X: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.37: 27 residues within 4Å: Chain 3: R.57, I.67, Y.74, T.75, M.79 Chain Y: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.38: 27 residues within 4Å: Chain Z: N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, S.126, V.127 Chain b: R.41, N.46, D.47, H.48, Y.175, A.176, T.177, S.178, R.180 Ligand excluded by PLIP CYC.39: 21 residues within 4Å: Chain 4: R.32, Q.33, D.145, D.148 Chain Y: F.28 Chain Z: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.40: 27 residues within 4Å: Chain 0: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, Y.90, Y.91, Y.110, I.115, I.118, F.122, L.124, W.128, Y.129 Chain Z: R.57, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.41: 27 residues within 4Å: Chain 1: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.91, Y.92, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: Q.92, N.93, Q.111, A.115, T.118, Y.121 Ligand excluded by PLIP CYC.42: 20 residues within 4Å: Chain 0: S.21, F.28 Chain 1: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, D.144, I.148, T.149, R.150, G.151, C.153 Chain 8: Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.43: 27 residues within 4Å: Chain 1: R.57, I.67, Y.74, T.75, S.76, M.79 Chain 2: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.44: 28 residues within 4Å: Chain 3: F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, S.126, V.127 Chain b: T.2, S.3, S.6, F.154, A.155, T.156, Q.160, K.161, T.162 Ligand excluded by PLIP CYC.45: 22 residues within 4Å: Chain 2: F.28 Chain 3: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Chain 6: Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.46: 31 residues within 4Å: Chain 4: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain 9: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.47: 25 residues within 4Å: Chain 5: L.59, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: R.24 Chain c: S.29, Q.30, I.41, R.42 Ligand excluded by PLIP CYC.48: 22 residues within 4Å: Chain 4: S.21, F.28 Chain 5: A.32, N.35, K.36, I.38, D.39, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Chain Y: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.49: 28 residues within 4Å: Chain 5: R.57, I.67, Y.74, T.75, S.76, M.79 Chain 6: V.59, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, I.94, Y.110, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.50: 29 residues within 4Å: Chain 7: L.59, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: T.9, S.11, L.53, M.56, N.57, M.60, R.61 Ligand excluded by PLIP CYC.51: 22 residues within 4Å: Chain 2: Q.33, D.145, D.148, E.149 Chain 6: F.28 Chain 7: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153, I.156 Ligand excluded by PLIP CYC.52: 29 residues within 4Å: Chain 7: R.57, I.67, Y.74, T.75, S.76, M.79 Chain 8: V.59, T.66, N.72, N.73, F.74, A.75, R.79, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.53: 24 residues within 4Å: Chain 9: L.59, L.66, N.72, A.73, R.78, C.82, R.84, D.85, M.86, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: S.57, S.60, L.61, R.63, G.64, E.66 Ligand excluded by PLIP CYC.54: 20 residues within 4Å: Chain 0: R.32, Q.33, D.145, D.148 Chain 8: F.28 Chain 9: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes. Nat Commun (2023)

Release Date

2023-11-08

Peptides

C-phycocyanin alpha subunit: ACEGIKMOQSUWY02468
C-phycocyanin beta subunit: BDFHJLNPRTVXZ13579
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1: a
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2: b
Ferredoxin--NADP reductase: c
Photosystem I-associated linker protein CpcL: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

Y
Y

0
a

2
c

4
e

6
g

8
i

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Z
Z

1
b

3
d

5
f

7
h

9
j

a
k

b
l

c
m

d
n

C-phycocyanin alpha subunit

C-phycocyanin beta subunit

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2

Ferredoxin--NADP reductase

Photosystem I-associated linker protein CpcL

Related Entries With Identical Sequence