SMTL ID : 8iml.1

Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-18-18-3-1-mer

Ligands

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

CYC.1: 28 residues within 4Å: Chain A: R.76, N.81, T.82, Y.83, Y.210, A.211, S.213, T.215, R.217 Chain M: L.66, N.72, R.77, R.78, A.81, C.82, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.2: 24 residues within 4Å: Chain B: V.60, F.61, V.67, K.73, G.74, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain H: H.57, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.3: 20 residues within 4Å: Chain B: R.34, Q.146, T.149, E.150, L.153 Chain C: L.25, F.29 Chain K: V.35, K.36, L.38, D.39, L.142, K.143, S.144, T.145, V.148, T.149, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.4: 24 residues within 4Å: Chain C: V.60, K.73, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.110, V.117, F.121, L.123, W.127, Y.128 Chain L: H.57, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.5: 18 residues within 4Å: Chain B: Q.26, F.29 Chain C: Q.146, T.149 Chain I: V.35, K.36, L.38, D.39, A.40, L.142, S.144, V.148, T.149, V.150, G.151, D.152, C.153, L.156 Ligand excluded by PLIP CYC.6: 21 residues within 4Å: Chain D: F.61, V.67, K.73, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, F.121, L.123, W.127, Y.128 Chain I: H.57, I.67, Y.74, H.76 Ligand excluded by PLIP CYC.7: 26 residues within 4Å: Chain E: V.60, F.61, V.67, K.73, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.110, V.117, F.121, L.123, W.127, Y.128 Chain M: H.57, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.8: 25 residues within 4Å: Chain F: V.60, F.61, V.67, K.73, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain J: H.57, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.9: 25 residues within 4Å: Chain G: V.60, F.61, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain K: H.57, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.10: 24 residues within 4Å: Chain H: L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, C.109, L.113, T.116, Y.117, L.120, S.126, V.127 Chain N: E.25, A.30, H.34, Y.38, I.42, R.43 Ligand excluded by PLIP CYC.11: 21 residues within 4Å: Chain F: L.25, Q.26, F.29 Chain G: R.34, Q.146, E.150, L.153 Chain H: V.35, K.36, D.39, A.40, L.142, K.143, S.144, T.145, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.12: 26 residues within 4Å: Chain I: 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, T.122, S.126, V.127 Chain N: Y.53, F.56, L.57, M.60, H.64 Ligand excluded by PLIP CYC.13: 25 residues within 4Å: Chain A: T.92, S.95, Q.96, K.98, D.99, R.101 Chain J: L.66, N.72, 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 Ligand excluded by PLIP CYC.14: 19 residues within 4Å: Chain D: L.25, Q.26, F.29 Chain E: Q.146, T.149, E.150 Chain J: V.35, K.36, L.38, D.39, A.40, L.142, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.15: 26 residues within 4Å: Chain A: F.189, K.190, Y.191, Q.195, Q.196, G.197, Y.200 Chain K: L.66, N.72, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.16: 24 residues within 4Å: Chain A: S.126, Q.127, N.128, Q.146, S.150, L.153 Chain L: N.72, 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, A.130 Ligand excluded by PLIP CYC.17: 21 residues within 4Å: Chain D: R.34, Q.146, T.149, E.150, L.153 Chain E: L.25, Q.26, F.29 Chain L: V.35, K.36, D.39, A.40, L.142, K.143, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.18: 19 residues within 4Å: Chain F: R.34, Q.146, E.150, L.153 Chain G: L.25, Q.26, F.29 Chain M: V.35, K.36, D.39, L.142, K.143, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.19: 24 residues within 4Å: Chain O: V.60, F.61, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain U: H.57, I.67, Y.74, H.76, M.79 Ligand excluded by PLIP CYC.20: 25 residues within 4Å: Chain P: V.60, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain Y: H.57, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.21: 27 residues within 4Å: Chain Q: V.60, F.61, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, I.87, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain V: H.57, F.60, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.22: 25 residues within 4Å: Chain R: V.60, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain Z: H.57, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.23: 26 residues within 4Å: Chain S: V.60, F.61, V.67, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, L.123, W.127, Y.128 Chain W: H.57, F.60, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.24: 24 residues within 4Å: Chain T: V.60, F.61, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain X: H.57, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.25: 27 residues within 4Å: Chain 0: Y.29, A.30, K.33, H.34, I.42, R.43, Q.44 Chain A: R.342 Chain U: 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, A.130 Ligand excluded by PLIP CYC.26: 22 residues within 4Å: Chain S: L.25, Q.26, F.29 Chain T: R.34, Q.146, T.149, E.150 Chain U: V.35, K.36, L.38, D.39, A.40, L.142, S.144, T.145, V.148, T.149, V.150, G.151, C.153, L.156, Y.157 Ligand excluded by PLIP CYC.27: 18 residues within 4Å: Chain O: L.25, F.29 Chain P: Q.146, T.149, L.153 Chain V: V.35, K.36, L.38, D.39, A.40, L.142, S.144, T.145, V.148, T.149, V.150, G.151, C.153 Ligand excluded by PLIP CYC.28: 24 residues within 4Å: Chain A: T.375, S.378, Q.379, K.381, D.382, R.384 Chain W: 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.29: 20 residues within 4Å: Chain Q: L.25, Q.26, F.29 Chain R: R.34, Q.146, L.153 Chain W: V.35, K.36, D.39, A.40, L.142, K.143, S.144, T.145, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.30: 29 residues within 4Å: Chain A: F.323, G.324, Q.325, F.472, K.473, Y.474, Q.478, A.480, F.483 Chain X: L.66, N.72, 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, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.31: 15 residues within 4Å: Chain O: Q.146, L.153 Chain P: Q.26, F.29 Chain X: V.35, K.36, D.39, L.142, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.32: 28 residues within 4Å: Chain A: S.409, Q.410, N.411, Q.429, I.432, S.433, L.436, W.439 Chain Y: L.66, N.72, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 Ligand excluded by PLIP CYC.33: 19 residues within 4Å: Chain Q: R.34, Q.146, T.149, E.150, L.153 Chain R: L.25, Q.26, F.29 Chain Y: V.35, K.36, D.39, L.142, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.34: 29 residues within 4Å: Chain A: R.359, N.364, T.365, Y.366, W.493, A.494, S.496, T.498, R.500 Chain Z: L.66, N.72, A.73, 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, V.127, A.130 Ligand excluded by PLIP CYC.35: 21 residues within 4Å: Chain S: R.34, Q.146, E.150, L.153 Chain T: L.25, Q.26, F.29 Chain Z: E.33, V.35, K.36, L.38, D.39, L.142, S.144, T.145, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.36: 24 residues within 4Å: Chain 0: Y.53, F.56, L.57, M.60, I.61, H.64 Chain V: N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.37: 20 residues within 4Å: Chain 1: S.71, R.74, N.75 Chain a: N.72, A.73, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Ligand excluded by PLIP CYC.38: 21 residues within 4Å: Chain 2: V.60, V.67, K.73, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, V.110, V.117, F.121, L.123, W.127, Y.128 Chain 8: F.60, I.67, Y.74, H.76 Ligand excluded by PLIP CYC.39: 23 residues within 4Å: Chain 3: V.60, F.61, V.67, K.73, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain c: H.57, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.40: 22 residues within 4Å: Chain 4: V.60, K.73, G.74, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain 9: H.57, I.67, Y.74, H.76, M.79 Ligand excluded by PLIP CYC.41: 24 residues within 4Å: Chain 5: V.60, K.73, G.74, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain d: H.57, F.60, I.67, Y.74, P.75, H.76, M.79 Ligand excluded by PLIP CYC.42: 23 residues within 4Å: Chain 6: V.60, K.73, G.74, N.79, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, Y.109, V.117, F.121, L.123, W.127, Y.128 Chain a: H.57, F.60, I.67, Y.74, H.76, M.79 Ligand excluded by PLIP CYC.43: 24 residues within 4Å: Chain 7: V.60, F.61, K.73, G.74, N.79, Q.80, K.82, C.83, R.85, D.86, Y.89, Y.90, F.93, V.117, F.121, L.123, W.127, Y.128 Chain b: H.57, F.60, I.67, Y.74, P.75, H.76 Ligand excluded by PLIP CYC.44: 19 residues within 4Å: Chain 8: A.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, C.109, L.113, T.116, Y.117, L.120, T.122, S.126, V.127 Chain e: H.34, Y.38, I.42 Ligand excluded by PLIP CYC.45: 13 residues within 4Å: Chain 6: Q.26, F.29 Chain 7: Q.146, L.153 Chain 8: V.35, K.36, D.39, T.145, V.148, T.149, V.150, G.151, C.153 Ligand excluded by PLIP CYC.46: 25 residues within 4Å: Chain 9: L.59, N.72, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, C.109, L.113, T.116, Y.117, L.120, T.122, V.127 Chain e: R.17, Y.53, F.56, L.57, M.60, I.61, H.64 Ligand excluded by PLIP CYC.47: 17 residues within 4Å: Chain 2: Q.26, F.29 Chain 3: Q.146, T.149 Chain 9: V.35, K.36, L.38, D.39, L.142, S.144, T.145, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.48: 19 residues within 4Å: Chain 4: Q.26, F.29 Chain 5: R.34, Q.146, E.150, L.153 Chain a: V.35, K.36, D.39, A.40, L.142, K.143, S.144, T.145, V.148, T.149, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.49: 27 residues within 4Å: Chain 1: S.12, K.13, P.14, R.16, V.17 Chain b: L.59, L.66, N.72, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 Ligand excluded by PLIP CYC.50: 14 residues within 4Å: Chain 2: Q.146, L.153 Chain 3: F.29 Chain b: V.35, K.36, D.39, L.142, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.51: 27 residues within 4Å: Chain 1: L.6, N.103, Y.104, I.126, K.127, S.129, I.130, A.133 Chain c: L.66, N.72, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, Y.117, L.120, T.122, S.126, V.127, A.130 Ligand excluded by PLIP CYC.52: 20 residues within 4Å: Chain 4: R.34, Q.146, T.149, E.150, L.153 Chain 5: L.25, Q.26, F.29 Chain c: K.36, L.38, D.39, L.142, S.144, T.145, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP CYC.53: 27 residues within 4Å: Chain 1: S.56, H.58, N.171, L.172, P.175, R.176, L.177 Chain d: L.66, N.72, R.77, R.78, A.81, C.82, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 Ligand excluded by PLIP CYC.54: 18 residues within 4Å: Chain 6: R.34, E.150, L.153 Chain 7: Q.26, F.29 Chain d: V.35, K.36, D.39, A.40, L.142, K.143, S.144, V.148, T.149, V.150, G.151, C.153, Y.157 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, H.W. et al., A structure of the relict phycobilisome from a thylakoid-free cyanobacterium. Nat Commun (2023)

Release Date

2023-10-25

Peptides

CpcJ: A
CpcA: BCDEFGOPQRST234567
CpcB: HIJKLMUVWXYZ89abcd
CpcD: N0e
CpcG: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
A

C
B

D
C

E
D

F
E

G
F

O
N

P
O

Q
P

R
Q

S
R

T
S

2
a

3
b

4
c

5
d

6
e

7
f

H
G

I
H

J
I

K
J

L
K

M
L

U
T

V
U

W
V

X
W

Y
X

Z
Y

8
g

9
h

a
i

b
j

c
k

d
l

N
M

0
Z

e
m

1
4

CpcJ

CpcA

CpcB

CpcD

CpcG

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