SMTL ID : 7veb.1

Phycocyanin rod structure of cyanobacterial phycobilisome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-1-1-1-mer

Ligands

36 x CYC: PHYCOCYANOBILIN(Non-covalent)

CYC.1: 17 residues within 4Å: Chain A: V.59, S.72, Q.73, Y.74, A.75, K.83, C.84, R.86, D.87, Y.90, Y.110, L.111, I.118, W.128, Y.129 Chain D: R.57, N.76 Ligand excluded by PLIP CYC.2: 25 residues within 4Å: Chain B: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, L.113, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 Chain Y: L.27, R.28, I.40, R.41, R.42, S.43 Ligand excluded by PLIP CYC.3: 20 residues within 4Å: Chain A: L.24, Q.25, D.28 Chain B: N.35, K.36, L.38, D.39, N.42, A.142, N.143, D.144, I.148, T.149, P.150, G.151, D.152, C.153, M.157 Chain E: R.33, Q.145 Ligand excluded by PLIP CYC.4: 23 residues within 4Å: Chain C: T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, Y.90, Y.91, M.94, Y.110, L.111, F.122, L.124, W.128, Y.129 Chain J: R.57, I.67, Y.74, T.75 Ligand excluded by PLIP CYC.5: 22 residues within 4Å: Chain D: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, Y.117, T.122, S.126, V.127, A.130 Chain Z: E.59, S.60, R.63, N.64 Ligand excluded by PLIP CYC.6: 16 residues within 4Å: Chain C: L.24, D.28 Chain D: N.35, K.36, L.38, D.39, N.143, P.145, I.148, T.149, P.150, G.151, C.153, M.157 Chain G: R.33, V.148 Ligand excluded by PLIP CYC.7: 26 residues within 4Å: Chain E: V.59, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain L: R.57, Y.74, T.75, N.76, M.79 Ligand excluded by PLIP CYC.8: 23 residues within 4Å: Chain F: N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, Y.92, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Chain Z: N.46, D.47, Y.48, Y.175, A.176, S.178 Ligand excluded by PLIP CYC.9: 18 residues within 4Å: Chain A: R.33, Q.145 Chain E: N.21, L.24, Q.25, D.28 Chain F: N.35, K.36, L.38, D.39, A.142, D.144, P.145, I.148, T.149, P.150, G.151, C.153 Ligand excluded by PLIP CYC.10: 26 residues within 4Å: Chain F: R.57, I.67, Y.74, T.75, N.76, M.79 Chain G: T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.11: 23 residues within 4Å: Chain H: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127, A.130 Chain Z: F.91, Q.92, T.93, I.115, L.118 Ligand excluded by PLIP CYC.12: 15 residues within 4Å: Chain G: N.21, Q.25, D.28 Chain H: N.35, K.36, D.39, N.42, A.142, N.143, D.144, P.145, I.148, T.149, G.151, C.153 Ligand excluded by PLIP CYC.13: 22 residues within 4Å: Chain B: R.57, Y.74 Chain I: V.59, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, L.111, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.14: 22 residues within 4Å: Chain J: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, L.113, Y.117, L.120, T.122, S.126, V.127 Chain Y: R.18, Y.52, M.55, N.56, Q.60 Ligand excluded by PLIP CYC.15: 18 residues within 4Å: Chain I: N.21, Q.25, D.28 Chain J: K.32, E.33, N.35, K.36, D.39, R.43, A.142, D.144, P.145, I.148, T.149, P.150, G.151, D.152, C.153 Ligand excluded by PLIP CYC.16: 24 residues within 4Å: Chain H: R.57, I.67, Y.74, T.75, N.76 Chain K: S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.17: 20 residues within 4Å: Chain L: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, L.113, L.120, T.122, P.123, S.126, V.127 Chain Z: A.6, F.154, T.156, Q.160 Ligand excluded by PLIP CYC.18: 17 residues within 4Å: Chain I: R.33, V.148, E.149 Chain K: D.28 Chain L: N.35, K.36, D.39, R.43, A.142, N.143, D.144, P.145, I.148, T.149, G.151, D.152, C.153 Ligand excluded by PLIP CYC.19: 24 residues within 4Å: Chain M: S.72, Q.73, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain P: R.57, Y.74, T.75, N.76, M.79 Ligand excluded by PLIP CYC.20: 25 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, I.88, Y.92, L.113, T.116, L.120, T.122, P.123, S.126, V.127 Chain Z: R.246, G.249, P.251, G.252, V.253, R.254 Ligand excluded by PLIP CYC.21: 18 residues within 4Å: Chain M: Q.25, D.28 Chain N: N.35, K.36, D.39, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, M.157 Chain Q: R.33, Q.145 Ligand excluded by PLIP CYC.22: 21 residues within 4Å: Chain O: S.72, Q.73, A.75, G.80, K.83, C.84, R.86, D.87, Y.90, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain V: R.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.23: 20 residues within 4Å: Chain 0: S.70, A.73, N.74 Chain P: L.59, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, I.88, R.108, Y.117, L.120, T.122, V.127 Chain Z: L.227, G.228 Ligand excluded by PLIP CYC.24: 17 residues within 4Å: Chain O: N.21, D.28 Chain P: N.35, K.36, L.38, D.39, A.142, D.144, I.148, T.149, P.150, G.151, D.152, C.153 Chain S: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.25: 25 residues within 4Å: Chain Q: V.59, T.66, S.72, Q.73, Y.74, A.75, K.83, C.84, R.86, D.87, I.88, Y.90, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Chain X: R.57, I.67, Y.74, T.75, N.76, M.79 Ligand excluded by PLIP CYC.26: 22 residues within 4Å: Chain 0: S.55, H.57, V.58, L.172, R.176 Chain R: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, L.113, Y.117, L.120, T.122, V.127 Ligand excluded by PLIP CYC.27: 17 residues within 4Å: Chain M: R.33, V.148 Chain Q: L.24, D.28 Chain R: N.35, K.36, L.38, D.39, A.142, N.143, D.144, I.148, T.149, P.150, G.151, C.153, M.157 Ligand excluded by PLIP CYC.28: 23 residues within 4Å: Chain R: R.57, Y.74, T.75, N.76, M.79 Chain S: V.59, T.66, S.72, Q.73, Y.74, A.75, K.83, C.84, R.86, D.87, Y.90, Y.91, Y.110, L.111, I.118, F.122, L.124, W.128 Ligand excluded by PLIP CYC.29: 25 residues within 4Å: Chain 0: L.6, N.102, Y.103, L.125, A.126, S.128, I.129, A.132 Chain T: L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, R.108, L.113, Y.117, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.30: 18 residues within 4Å: Chain O: R.33, Q.145 Chain S: L.24, Q.25, D.28 Chain T: N.35, K.36, L.38, D.39, A.40, N.42, R.43, P.145, I.148, T.149, P.150, G.151, C.153 Ligand excluded by PLIP CYC.31: 25 residues within 4Å: Chain N: R.57, I.67, Y.74, T.75, M.79 Chain U: V.59, S.72, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, Y.90, Y.91, R.93, M.94, Y.110, L.111, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.32: 22 residues within 4Å: Chain V: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Chain Z: Y.264, L.267, S.268, Q.272 Ligand excluded by PLIP CYC.33: 17 residues within 4Å: Chain U: Q.25, D.28 Chain V: K.32, N.35, K.36, D.39, A.142, N.143, D.144, P.145, I.148, T.149, G.151, D.152, C.153, M.157 Chain W: R.33 Ligand excluded by PLIP CYC.34: 23 residues within 4Å: Chain T: R.57, I.67, Y.74, T.75, M.79 Chain W: V.59, S.72, Y.74, A.75, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, R.93, M.94, Y.110, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.35: 21 residues within 4Å: Chain 0: S.12, Q.13, N.14, R.16, V.17, A.18, Y.165 Chain X: N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, L.113, T.116, Y.117, T.122, V.127 Ligand excluded by PLIP CYC.36: 19 residues within 4Å: Chain W: L.24, Q.25, D.28 Chain X: N.35, K.36, L.38, D.39, A.40, N.42, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, M.157 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawakami, K. et al., Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome. Nat Commun (2022)

Release Date

2022-06-15

Peptides

C-phycocyanin alpha subunit: ACEGIKMOQSUW
C-phycocyanin beta subunit: BDFHJLNPRTVX
Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod: Y
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod: Z
Phycobilisome rod-core linker polypeptide CpcG2: 0

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

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Y
Y

Z
Z

0
a

C-phycocyanin alpha subunit

C-phycocyanin beta subunit

Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

Phycobilisome rod-core linker polypeptide CpcG2

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