SMTL ID : 9i1r.1

Structure of the bicylindrical allophycocyanin core expressed during far-red light photoacclimation (FaRLiP)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.51 Å

Oligo State

hetero-18-22-2-2-2-2-2-mer

Ligands

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

CYC.1: 26 residues within 4Å: Chain A: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain F: L.61, Y.62, T.66, Y.73, T.74, C.75 Ligand excluded by PLIP CYC.2: 26 residues within 4Å: Chain B: L.60, N.71, M.72, R.77, A.80, C.81, D.84, L.85, Y.87, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Chain S: P.11, S.12, R.15, L.22, Q.23, N.24, T.25 Ligand excluded by PLIP CYC.3: 26 residues within 4Å: Chain B: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain C: F.58, T.65, P.66, S.67, K.74, A.77, A.78, R.80, D.81, W.84, Y.85, I.104, L.112, Y.113, V.116, I.118, N.122, V.123, Y.126 Ligand excluded by PLIP CYC.4: 30 residues within 4Å: Chain D: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Chain S: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44 Ligand excluded by PLIP CYC.5: 27 residues within 4Å: Chain D: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain E: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.6: 25 residues within 4Å: Chain F: L.60, I.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, L.119, V.121, P.122, A.125, T.126 Chain K: E.323, S.326, Q.327, I.329, G.330 Ligand excluded by PLIP CYC.7: 27 residues within 4Å: Chain G: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain L: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.8: 28 residues within 4Å: Chain H: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Chain K: I.358, S.359, R.377, F.380, Q.381, F.384 Ligand excluded by PLIP CYC.9: 28 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain I: F.58, T.65, P.66, S.67, Y.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, L.88, I.104, G.105, M.112, Y.113, L.116, I.118, N.122, W.123, C.126 Ligand excluded by PLIP CYC.10: 33 residues within 4Å: Chain J: N.72, R.77, R.78, M.81, Y.82, R.84, D.85, M.86, Y.88, F.89, Y.92, R.108, L.109, L.113, T.116, F.117, L.120, I.122, P.123, P.126, T.127, S.130 Chain K: P.14, Q.267, L.269, L.271, Y.275, L.420, E.423, A.424, Q.425, E.426, C.427 Ligand excluded by PLIP CYC.11: 26 residues within 4Å: Chain C: Y.164, F.165, Q.166 Chain J: V.67, T.75, T.76 Chain K: I.75, I.158, Y.163, R.167, R.170, S.171, R.173, D.174, L.175, W.177, F.178, Y.181, N.197, V.198, L.201, V.204, I.205, P.206, V.209, T.213 Ligand excluded by PLIP CYC.12: 22 residues within 4Å: Chain K: Y.439 Chain L: N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, Y.91, R.107, I.108, L.112, T.115, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.13: 27 residues within 4Å: Chain M: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain R: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.14: 22 residues within 4Å: Chain N: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.15: 27 residues within 4Å: Chain N: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain O: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.16: 27 residues within 4Å: Chain K: S.553, S.589, S.592, G.596, E.598 Chain P: L.60, I.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, I.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Ligand excluded by PLIP CYC.17: 26 residues within 4Å: Chain P: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain Q: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.18: 23 residues within 4Å: Chain R: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.19: 27 residues within 4Å: Chain T: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain Y: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.20: 27 residues within 4Å: Chain K: I.475, Q.476, F.477, G.478, R.577 Chain U: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, I.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.21: 26 residues within 4Å: Chain U: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain V: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.22: 27 residues within 4Å: Chain K: Y.466, Y.623, V.624, T.625, R.643, N.647, Y.650 Chain W: L.60, I.65, N.71, M.72, R.77, A.80, C.81, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.23: 31 residues within 4Å: Chain K: G.93, L.94, P.95 Chain W: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain X: F.58, T.65, P.66, S.67, R.73, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.24: 27 residues within 4Å: Chain K: I.502, L.503, I.504, G.505, G.520 Chain Y: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.25: 26 residues within 4Å: Chain 4: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain Z: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.26: 25 residues within 4Å: Chain 0: L.60, N.71, R.77, A.80, C.81, D.84, L.85, Y.87, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Chain h: P.11, S.12, R.15, L.22, Q.23, N.24, T.25 Ligand excluded by PLIP CYC.27: 25 residues within 4Å: Chain 0: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain 1: F.58, T.65, P.66, S.67, K.74, A.77, A.78, R.80, D.81, W.84, Y.85, I.104, L.112, Y.113, V.116, I.118, N.122, V.123, Y.126 Ligand excluded by PLIP CYC.28: 31 residues within 4Å: Chain 2: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Chain h: R.2, Y.33, W.36, F.37, Q.40, Q.41, M.44 Ligand excluded by PLIP CYC.29: 27 residues within 4Å: Chain 2: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain 3: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.30: 27 residues within 4Å: Chain 4: L.60, I.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Chain 9: E.323, S.326, Q.327, I.329, G.330 Ligand excluded by PLIP CYC.31: 27 residues within 4Å: Chain 5: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain a: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.32: 27 residues within 4Å: Chain 6: L.60, I.65, N.71, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Chain 9: I.358, S.359, R.377, F.380, Q.381, F.384 Ligand excluded by PLIP CYC.33: 28 residues within 4Å: Chain 6: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain 7: F.58, T.65, P.66, S.67, Y.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, L.88, I.104, G.105, M.112, Y.113, L.116, I.118, N.122, W.123, C.126 Ligand excluded by PLIP CYC.34: 33 residues within 4Å: Chain 8: N.72, R.77, R.78, M.81, Y.82, R.84, D.85, M.86, Y.88, F.89, Y.92, R.108, L.109, L.113, T.116, F.117, L.120, I.122, P.123, P.126, T.127, S.130 Chain 9: P.14, Q.267, L.269, L.271, Y.275, L.420, E.423, A.424, Q.425, E.426, C.427 Ligand excluded by PLIP CYC.35: 26 residues within 4Å: Chain 1: Y.164, F.165, Q.166 Chain 8: V.67, T.75, T.76 Chain 9: I.75, I.158, Y.163, R.167, R.170, S.171, R.173, D.174, L.175, W.177, F.178, Y.181, N.197, V.198, L.201, V.204, I.205, P.206, V.209, T.213 Ligand excluded by PLIP CYC.36: 21 residues within 4Å: Chain 9: Y.439 Chain a: N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, T.115, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.37: 27 residues within 4Å: Chain b: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain g: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.38: 22 residues within 4Å: Chain c: L.60, I.65, N.71, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.39: 27 residues within 4Å: Chain c: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain d: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.40: 26 residues within 4Å: Chain 9: S.553, S.589, S.592, G.596, E.598 Chain e: L.60, I.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126, S.129 Ligand excluded by PLIP CYC.41: 26 residues within 4Å: Chain e: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain f: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.42: 23 residues within 4Å: Chain g: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, F.88, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.43: 27 residues within 4Å: Chain i: F.58, T.65, P.66, S.67, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Chain n: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Ligand excluded by PLIP CYC.44: 27 residues within 4Å: Chain 9: I.475, Q.476, F.477, G.478, R.577 Chain j: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, R.107, I.108, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.45: 27 residues within 4Å: Chain j: L.61, Y.62, T.66, Y.73, T.74, C.75 Chain k: F.58, T.65, P.66, S.67, R.73, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.46: 27 residues within 4Å: Chain 9: Y.466, Y.623, V.624, T.625, R.643, N.647, Y.650 Chain l: L.60, I.65, N.71, M.72, R.77, A.80, C.81, D.84, L.85, Y.87, F.88, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP CYC.47: 31 residues within 4Å: Chain 9: G.93, L.94, P.95 Chain l: L.61, Y.62, T.66, Y.73, T.74, C.75, Y.78 Chain m: F.58, T.65, P.66, S.67, R.73, K.74, S.77, C.78, R.80, D.81, Q.82, W.84, Y.85, I.104, M.112, Y.113, L.116, I.118, N.122, I.123, C.126 Ligand excluded by PLIP CYC.48: 27 residues within 4Å: Chain 9: I.502, L.503, I.504, G.505, G.520 Chain n: L.60, I.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.91, R.107, I.108, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Consoli, G. et al., Structure of a stripped-down and tuned-up far-red phycobilisome. Commun Biol (2025)

Release Date

2025-07-02

Peptides

Phycocyanin: AEGMOQTVXZ35bdfikm
Allophycocyanin beta subunit apoprotein: BDFHLNPRUWY0246acegjln
Phycocyanin: C1
Phycocyanin: I7
Allophycocyanin beta-18 subunit apoprotein: J8
Phycobiliprotein ApcE: K9
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: Sh

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

G
G

M
M

O
O

Q
Q

T
T

V
V

X
X

Z
a

3
e

5
g

b
m

d
o

f
q

i
t

k
v

m
x

B
B

D
D

F
F

H
H

L
L

N
N

P
P

R
R

U
U

W
W

Y
Y

0
b

2
d

4
f

6
h

a
l

c
n

e
p

g
r

j
u

l
w

n
y

C
C

1
c

I
I

7
i

J
J

8
j

K
K

9
k

S
S

h
s

Phycocyanin

Allophycocyanin beta subunit apoprotein

Phycocyanin

Phycocyanin

Allophycocyanin beta-18 subunit apoprotein

Phycobiliprotein ApcE

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core