SMTL ID : 9v7i.1

Phycobilisome rod R3 from Gloeobacter violaceus PCC 7421

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.03 Å

Oligo State

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

Ligands

36 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 22 residues within 4Å: Chain A: H.29, T.36, H.37, P.39 Chain B: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.2: 17 residues within 4Å: Chain B: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain E: R.33, Q.145, E.149 Chain Z: L.24, N.28 Ligand excluded by PLIP CYC.3: 22 residues within 4Å: Chain C: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain F: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.4: 26 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, T.122, S.126, V.127 Chain M: S.161, N.162, N.163, A.185, L.188, R.271 Ligand excluded by PLIP CYC.5: 16 residues within 4Å: Chain C: L.24, N.28 Chain D: N.35, K.36, L.38, D.39, V.142, P.145, V.148, T.149, R.150, G.151, C.153 Chain G: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.6: 22 residues within 4Å: Chain E: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain L: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.7: 19 residues within 4Å: Chain F: N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, L.113, Y.117, L.120, T.122, S.126, V.127 Chain M: N.116, Y.118, A.246, L.252 Ligand excluded by PLIP CYC.8: 16 residues within 4Å: Chain E: L.24, N.28 Chain F: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain Z: R.33, Q.145 Ligand excluded by PLIP CYC.9: 22 residues within 4Å: Chain G: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain J: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.10: 25 residues within 4Å: Chain A: T.5, G.6 Chain H: 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, T.122, S.126, V.127, A.130 Chain M: S.130, L.131, N.134 Ligand excluded by PLIP CYC.11: 18 residues within 4Å: Chain C: R.33, Q.145, E.149 Chain G: N.21, L.24, N.28 Chain H: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.12: 22 residues within 4Å: Chain B: H.57, I.67, Y.74, P.75, N.76 Chain I: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.13: 22 residues within 4Å: Chain A: L.50, L.53, L.54, M.57 Chain J: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.14: 17 residues within 4Å: Chain I: L.24, N.28 Chain J: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain K: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.15: 23 residues within 4Å: Chain D: H.57, Y.74, P.75, N.76, M.79 Chain K: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, Y.108, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.16: 22 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, C.109, L.113, Y.117, L.120, T.122, S.126, V.127 Chain M: F.224, K.225, Q.230, V.232 Ligand excluded by PLIP CYC.17: 17 residues within 4Å: Chain I: R.33, Q.145, E.149 Chain K: L.24, N.28 Chain L: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.18: 22 residues within 4Å: Chain N: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain U: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.19: 23 residues within 4Å: Chain 0: S.680, L.681, R.683, N.684 Chain M: L.4 Chain O: 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, T.116, Y.117, L.120, T.122, S.126 Ligand excluded by PLIP CYC.20: 16 residues within 4Å: Chain N: L.24, N.28 Chain O: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain R: R.33, Q.145 Ligand excluded by PLIP CYC.21: 19 residues within 4Å: Chain P: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, F.120, L.122, W.126 Chain S: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.22: 25 residues within 4Å: Chain 0: A.626, Q.627, F.774, K.775, Y.776, Q.780, A.782 Chain Q: 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, T.122, S.126, V.127 Ligand excluded by PLIP CYC.23: 16 residues within 4Å: Chain P: L.24, N.28 Chain Q: N.35, K.36, L.38, D.39, V.142, P.145, V.148, T.149, R.150, G.151, C.153 Chain T: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.24: 21 residues within 4Å: Chain R: Y.60, L.66, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Chain Y: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.25: 22 residues within 4Å: Chain 0: N.712, N.713, Q.731, V.735, L.738, R.821 Chain S: N.72, A.73, R.77, R.78, C.82, R.84, D.85, M.86, I.88, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.26: 16 residues within 4Å: Chain N: R.33, Q.145 Chain R: L.24, N.28 Chain S: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.27: 21 residues within 4Å: Chain T: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, V.116, F.120, L.122, W.126, Y.127 Chain W: H.57, I.67, Y.74, N.76 Ligand excluded by PLIP CYC.28: 20 residues within 4Å: Chain M: L.49, M.56, K.60 Chain U: N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.29: 18 residues within 4Å: Chain P: R.33, Q.145, E.149 Chain T: N.21, L.24, N.28 Chain U: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.30: 23 residues within 4Å: Chain O: H.57, I.67, Y.74, P.75, N.76 Chain V: Y.60, L.66, M.72, G.73, N.78, Q.79, K.81, C.82, R.84, D.85, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.31: 23 residues within 4Å: Chain M: P.23, D.34, T.35, Y.36, P.38 Chain W: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.108, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.32: 17 residues within 4Å: Chain V: L.24, N.28 Chain W: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Chain X: R.33, Q.145, E.149 Ligand excluded by PLIP CYC.33: 19 residues within 4Å: Chain Q: H.57, I.67, Y.74, N.76 Chain X: Y.60, L.66, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP CYC.34: 24 residues within 4Å: Chain 0: N.666, T.667, Y.668, A.796, S.798, T.800, R.802 Chain Y: L.66, N.72, R.77, R.78, A.81, C.82, D.85, M.86, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126 Ligand excluded by PLIP CYC.35: 17 residues within 4Å: Chain V: R.33, Q.145, E.149 Chain X: L.24, N.28 Chain Y: N.35, K.36, L.38, D.39, V.142, N.143, P.145, V.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.36: 22 residues within 4Å: Chain H: H.57, I.67, Y.74, N.76 Chain Z: Y.60, L.66, M.72, G.73, N.78, K.81, C.82, R.84, D.85, H.88, Y.89, F.92, I.109, V.116, F.120, L.122, W.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burtseva, A.D. et al., Structure and quenching of a bundle-shaped phycobilisome. Sci Adv (2025)

Release Date

2025-09-24

Peptides

Phycobilisome rod linker polypeptide CpcC1: A
Phycocyanin beta chain: BDFHJLOQSUWY
Phycocyanin alpha chain: CEGIKNPRTVXZ
Phycobilisome rod linker polypeptide CpcC2: M
Glr1262 protein: 0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

F
F

H
H

J
J

L
L

O
O

Q
Q

S
S

U
U

W
W

Y
Y

C
C

E
E

G
G

I
I

K
K

N
N

P
P

R
R

T
T

V
V

X
X

Z
a

M
M

0
Z

Phycobilisome rod linker polypeptide CpcC1

Phycocyanin beta chain

Phycocyanin alpha chain

Phycobilisome rod linker polypeptide CpcC2

Glr1262 protein

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