SMTL ID : 8to5.1

Central rod disk in C1 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-1-1-mer

Ligands

18 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 33 residues within 4Å: Chain A: 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, F.122, L.124, W.128, Y.129, A.132 Chain F: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.2: 30 residues within 4Å: Chain B: L.59, F.60, 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, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain N: R.219, Y.250, L.253, S.254, L.257, Q.258, N.261 Ligand excluded by PLIP CYC.3: 27 residues within 4Å: Chain A: S.21, L.24, Q.25, 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, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Chain G: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.4: 32 residues within 4Å: Chain B: R.57, F.60, 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, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.5: 32 residues within 4Å: Chain D: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain M: G.57, S.60, L.61, T.63, N.64 Chain N: L.211, G.213 Ligand excluded by PLIP CYC.6: 27 residues within 4Å: Chain C: S.21, L.24, Q.25, F.28 Chain D: 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, I.156, V.157 Chain K: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.7: 33 residues within 4Å: Chain D: R.57, F.60, 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, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Ligand excluded by PLIP CYC.8: 34 residues within 4Å: Chain F: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, R.91, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain M: R.24 Chain N: G.230, A.231, R.238, V.239, R.240, R.241, G.242 Ligand excluded by PLIP CYC.9: 27 residues within 4Å: Chain E: S.21, L.24, Q.25, F.28 Chain F: 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, D.152, C.153 Chain I: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.10: 33 residues within 4Å: Chain G: 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, F.122, L.124, W.128, Y.129, A.132 Chain L: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.11: 37 residues within 4Å: Chain H: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, R.91, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain M: A.2, I.3, T.4, T.5, A.6, F.153, N.154, N.155, D.159, R.160, T.161, F.164 Ligand excluded by PLIP CYC.12: 27 residues within 4Å: Chain A: R.32, Q.33, D.145, D.148, E.149 Chain G: S.21, L.24, Q.25, 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, P.145, I.148, T.149, R.150, G.151, D.152, C.153 Ligand excluded by PLIP CYC.13: 32 residues within 4Å: Chain H: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain I: 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, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.14: 33 residues within 4Å: Chain J: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain M: R.41, N.46, D.47, Y.48, Y.174, A.175, N.176, S.177, S.180 Ligand excluded by PLIP CYC.15: 26 residues within 4Å: Chain E: R.32, Q.33, D.145, D.148, E.149 Chain I: S.21, 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, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Ligand excluded by PLIP CYC.16: 32 residues within 4Å: Chain J: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain K: 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, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.17: 33 residues within 4Å: Chain L: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain M: F.91, Q.92, T.93, E.111, V.114, I.115, L.118, Y.121 Ligand excluded by PLIP CYC.18: 27 residues within 4Å: Chain C: R.32, Q.33, D.145, D.148, E.149 Chain K: S.21, L.24, Q.25, 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, P.145, I.148, T.149, R.150, G.151, D.152, C.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauer, P.V. et al., Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Sci Adv (2024)

Release Date

2024-04-17

Peptides

C-phycocyanin alpha subunit: ACEGIK
C-phycocyanin beta subunit: BDFHJL
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1: M
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

C
O

E
Q

G
S

I
U

K
W

B
N

D
P

F
R

H
T

J
V

L
X

M
b

N
c

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

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