9WG7 | pdb_00009wg7

The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942.

Zheng, Z.Ma, C.Wang, H.Wang, G.Dong, C.Gao, N.Zhao, J.

(2025) Photosynth Res 163: 65-65

  • DOI: https://doi.org/10.1007/s11120-025-01186-x
  • Primary Citation Related Structures: 
    9WG7, 9X69, 9X6D

  • PubMed Abstract: 

    Phycobilisomes (PBSs) are the major light-harvesting complexes in the cyanobacteria and red algae and they consist of a central core and peripheral rods that are attached to the core. The PBS cores contain 2-5 allophycocyanin cylinders that are organized by ApcE. At the present, structures of PBS with tricylindrical and pentacylindrical cores have been determined while the structure of the PBS with a bicylindrical core is yet to be revealed. Here we report the cryo-EM structure of PBS with bicylindrical core from Synechococcus elongatus PCC 7942 (Synechococcus 7942) at an overall resolution of approximately 3 Å. Similar to the PBS with a tricylindrical core, six peripheral rods are attached to the core by the rod-core linker protein CpcG in the PBS of Synechococcus 7942 even though the core lacks the top AP cylinder, which is important for the attachment of peripheral rods to the tricylindrical cores. We found that the C-terminus of ApcE in the Synechococcus 7942 was involved in interacting with both CpcG and CpcB of a top peripheral rod, compensating for the absence of the top AP cylinder of the core and maintaining PBS stability. Analysis of the bilin distribution reveals that distance of excitation energy transfer from top peripheral rods to the terminal emitters is approximately 15% shorter compared to the PBS with tricylindrical cores. Although there are 30% fewer bilin chromophores in the Synechococcus 7942 PBS core compared with the tricylindrical core, the aromatic residue ring in the Synechococcus 7942 PBS core is conserved, supporting the suggestion that these aromatic residues from AP and linker proteins are critical to the energy transfer of PBS.


  • Organizational Affiliation
    • State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, 100871, P. R. China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide250Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31LK9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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UniProt GroupQ31LK9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit163Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for P13530 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit173Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for P06539 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod linker polypeptide273Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31PE0 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod linker polypeptide289Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31PD9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, coreBA [auth 02],
FB [auth Y2],
GB [auth Z2],
GC [auth z2]
67Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31RG2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ApcGCA [auth 12],
IB [auth b2]
110Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31RM8 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin, beta subunit161Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31RG1 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha chain161Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcEUA [auth N2],
VB [auth o2]
705Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31RF9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin, beta subunitWA [auth P2],
XB [auth q2]
169Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for O50209 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha-B chainAC [auth t2],
ZA [auth S2]
163Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for Q31RP7 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download Ideal Coordinates CCD File 
AI [auth P1]
AJ [auth B2]
AK [auth f2]
AL [auth F3]
AM [auth B4]
AI [auth P1],
AJ [auth B2],
AK [auth f2],
AL [auth F3],
AM [auth B4],
AN [auth V4],
AO [auth R5],
AP [auth K6],
AQ [auth F7],
BI [auth P1],
BJ [auth B2],
BK [auth g2],
BL [auth G3],
BM [auth C4],
BN [auth W4],
BO [auth S5],
BP [auth L6],
BQ [auth G7],
CI [auth Q1],
CJ [auth C2],
CK [auth h2],
CL [auth H3],
CM [auth C4],
CN [auth X4],
CO [auth T5],
CP [auth M6],
CQ [auth H7],
DI [auth Q1],
DJ [auth D2],
DK [auth i2],
DL [auth I3],
DM [auth D4],
DN [auth Z4],
DO [auth T5],
DP [auth N6],
DQ [auth I7],
EI [auth R1],
EJ [auth E2],
EK [auth j2],
EL [auth J3],
EM [auth E4],
EN [auth a4],
EO [auth U5],
EP [auth P6],
EQ [auth J7],
FI [auth S1],
FJ [auth F2],
FK [auth k2],
FL [auth J3],
FM [auth F4],
FN [auth a4],
FO [auth V5],
FP [auth P6],
FQ [auth J7],
GI [auth T1],
GJ [auth G2],
GK [auth l2],
GL [auth K3],
GM [auth F4],
GN [auth B5],
GO [auth V5],
GP [auth Q6],
GQ [auth K7],
HI [auth T1],
HJ [auth H2],
HK [auth m2],
HL [auth L3],
HM [auth G4],
HN [auth C5],
HO [auth W5],
HP [auth Q6],
HQ [auth L7],
IH [auth A1],
II [auth U1],
IJ [auth L2],
IK [auth n2],
IL [auth M3],
IM [auth H4],
IN [auth C5],
IO [auth X5],
IP [auth R6],
IQ [auth M7],
JH [auth A1],
JI [auth V1],
JJ [auth M2],
JK [auth o2],
JL [auth N3],
JM [auth I4],
JN [auth D5],
JO [auth Z5],
JP [auth S6],
JQ [auth N7],
KH [auth B1],
KI [auth V1],
KJ [auth N2],
KK [auth p2],
KL [auth P3],
KM [auth J4],
KN [auth E5],
KO [auth a5],
KP [auth T6],
KQ [auth P7],
LH [auth C1],
LI [auth W1],
LJ [auth N2],
LK [auth q2],
LL [auth P3],
LM [auth J4],
LN [auth F5],
LO [auth a5],
LP [auth T6],
LQ [auth P7],
MH [auth C1],
MI [auth X1],
MJ [auth O2],
MK [auth r2],
ML [auth Q3],
MM [auth K4],
MN [auth F5],
MO [auth A6],
MP [auth U6],
MQ [auth Q7],
NH [auth D1],
NI [auth Z1],
NJ [auth P2],
NK [auth s2],
NL [auth Q3],
NM [auth L4],
NN [auth G5],
NO [auth A6],
NP [auth V6],
NQ [auth Q7],
OH [auth E1],
OI [auth a1],
OJ [auth Q2],
OK [auth t2],
OL [auth R3],
OM [auth M4],
ON [auth H5],
OO [auth B6],
OP [auth V6],
OQ [auth R7],
PH [auth F1],
PI [auth a1],
PJ [auth R2],
PK [auth v2],
PL [auth S3],
PM [auth N4],
PN [auth I5],
PO [auth C6],
PP [auth W6],
PQ [auth S7],
QH [auth F1],
QI [auth 22],
QJ [auth S2],
QK [auth w2],
QL [auth T3],
QM [auth P4],
QN [auth J5],
QO [auth C6],
QP [auth X6],
QQ [auth T7],
RH [auth G1],
RI [auth 22],
RJ [auth T2],
RK [auth x2],
RL [auth T3],
RM [auth P4],
RN [auth J5],
RO [auth D6],
RP [auth Z6],
RQ [auth T7],
SH [auth H1],
SI [auth 32],
SJ [auth U2],
SK [auth y2],
SL [auth U3],
SM [auth Q4],
SN [auth K5],
SO [auth E6],
SP [auth a6],
SQ [auth U7],
TH [auth I1],
TI [auth 32],
TJ [auth V2],
TK [auth z2],
TL [auth V3],
TM [auth Q4],
TN [auth L5],
TO [auth F6],
TP [auth a6],
TQ [auth V7],
UH [auth J1],
UI [auth 42],
UJ [auth W2],
UK [auth B3],
UL [auth V3],
UM [auth R4],
UN [auth M5],
UO [auth F6],
UP [auth B7],
UQ [auth V7],
VH [auth J1],
VI [auth 42],
VJ [auth X2],
VK [auth C3],
VL [auth W3],
VM [auth S4],
VN [auth N5],
VO [auth G6],
VP [auth C7],
VQ [auth W7],
WH [auth K1],
WI [auth 52],
WJ [auth a2],
WK [auth C3],
WL [auth X3],
WM [auth T4],
WN [auth P5],
WO [auth H6],
WP [auth C7],
WQ [auth X7],
XH [auth L1],
XI [auth 52],
XJ [auth c2],
XK [auth D3],
XL [auth Z3],
XM [auth T4],
XN [auth P5],
XO [auth I6],
XP [auth D7],
XQ [auth Z7],
YH [auth M1],
YI [auth A2],
YJ [auth d2],
YK [auth E3],
YL [auth a3],
YM [auth U4],
YN [auth Q5],
YO [auth J6],
YP [auth E7],
YQ [auth a7],
ZH [auth N1],
ZI [auth A2],
ZJ [auth e2],
ZK [auth F3],
ZL [auth a3],
ZM [auth V4],
ZN [auth Q5],
ZO [auth J6],
ZP [auth F7],
ZQ [auth a7]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONUCSF ChimeraX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release