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- PDB-9wg7: The structure of phycobilisome with a bicylindrical core from the... -

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Basic information

Entry
Database: PDB / ID: 9wg7
TitleThe structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942
Components
  • (Allophycocyanin ...) x 2
  • (Allophycocyanin, beta ...) x 2
  • (C-phycocyanin ...) x 2
  • (Phycobilisome ...) x 4
  • ApcG
  • Phycobiliprotein ApcE
KeywordsELECTRON TRANSPORT / PBS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin, beta subunit / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / Phycobilisome rod linker polypeptide / Phycobilisome rod linker polypeptide / Phycobiliprotein ApcE / Allophycocyanin alpha chain / Allophycocyanin, beta subunit ...PHYCOCYANOBILIN / Allophycocyanin, beta subunit / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / Phycobilisome rod linker polypeptide / Phycobilisome rod linker polypeptide / Phycobiliprotein ApcE / Allophycocyanin alpha chain / Allophycocyanin, beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Uncharacterized protein / Allophycocyanin alpha-B chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng, Z.G. / Ma, C.Y. / Wang, H.R. / Wang, G.P. / Dong, C.X. / Gao, N. / Zhao, J.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Photosynth Res / Year: 2025
Title: The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942.
Authors: Zhenggao Zheng / Chengying Ma / Hongrui Wang / Guopeng Wang / Chunxia Dong / Ning Gao / Jindong Zhao /
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 ...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.
History
DepositionAug 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Phycobilisome rod-core linker polypeptide
B1: C-phycocyanin alpha subunit
C1: C-phycocyanin beta subunit
D1: C-phycocyanin beta subunit
E1: C-phycocyanin beta subunit
F1: C-phycocyanin alpha subunit
G1: C-phycocyanin alpha subunit
H1: C-phycocyanin alpha subunit
I1: C-phycocyanin alpha subunit
J1: C-phycocyanin beta subunit
K1: C-phycocyanin alpha subunit
L1: C-phycocyanin beta subunit
M1: C-phycocyanin beta subunit
N1: C-phycocyanin alpha subunit
O1: C-phycocyanin beta subunit
P1: C-phycocyanin beta subunit
Q1: C-phycocyanin beta subunit
R1: C-phycocyanin alpha subunit
S1: C-phycocyanin alpha subunit
T1: C-phycocyanin alpha subunit
U1: C-phycocyanin alpha subunit
V1: C-phycocyanin beta subunit
W1: C-phycocyanin alpha subunit
X1: C-phycocyanin beta subunit
Y1: Phycobilisome rod linker polypeptide
Z1: Phycobilisome rod linker polypeptide
a1: C-phycocyanin beta subunit
02: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
12: ApcG
22: Phycobilisome rod-core linker polypeptide
32: Phycobilisome rod-core linker polypeptide
42: Phycobilisome rod-core linker polypeptide
52: Phycobilisome rod-core linker polypeptide
A2: Allophycocyanin, beta subunit
B2: Allophycocyanin, beta subunit
C2: Allophycocyanin, beta subunit
D2: Allophycocyanin alpha chain
E2: Allophycocyanin alpha chain
F2: Allophycocyanin, beta subunit
G2: Allophycocyanin alpha chain
H2: Allophycocyanin alpha chain
I2: Allophycocyanin alpha chain
J2: Allophycocyanin alpha chain
K2: Allophycocyanin, beta subunit
L2: Allophycocyanin, beta subunit
M2: Allophycocyanin, beta subunit
N2: Phycobiliprotein ApcE
O2: Allophycocyanin, beta subunit
P2: Allophycocyanin, beta subunit
Q2: Allophycocyanin alpha chain
R2: Allophycocyanin alpha chain
S2: Allophycocyanin alpha-B chain
T2: Allophycocyanin, beta subunit
U2: Allophycocyanin alpha chain
V2: Allophycocyanin, beta subunit
W2: Allophycocyanin alpha chain
X2: Allophycocyanin, beta subunit
Y2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Z2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
a2: Allophycocyanin, beta subunit
b2: ApcG
c2: Allophycocyanin, beta subunit
d2: Allophycocyanin, beta subunit
e2: Allophycocyanin alpha chain
f2: Allophycocyanin alpha chain
g2: Allophycocyanin, beta subunit
h2: Allophycocyanin alpha chain
i2: Allophycocyanin alpha chain
j2: Allophycocyanin alpha chain
k2: Allophycocyanin alpha chain
l2: Allophycocyanin, beta subunit
m2: Allophycocyanin, beta subunit
n2: Allophycocyanin, beta subunit
o2: Phycobiliprotein ApcE
p2: Allophycocyanin, beta subunit
q2: Allophycocyanin, beta subunit
r2: Allophycocyanin alpha chain
s2: Allophycocyanin alpha chain
t2: Allophycocyanin alpha-B chain
u2: Allophycocyanin, beta subunit
v2: Allophycocyanin alpha chain
w2: Allophycocyanin, beta subunit
x2: Allophycocyanin alpha chain
y2: Allophycocyanin, beta subunit
z2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
B3: C-phycocyanin alpha subunit
C3: C-phycocyanin beta subunit
D3: C-phycocyanin beta subunit
E3: C-phycocyanin beta subunit
F3: C-phycocyanin alpha subunit
G3: C-phycocyanin alpha subunit
H3: C-phycocyanin alpha subunit
I3: C-phycocyanin alpha subunit
J3: C-phycocyanin beta subunit
K3: C-phycocyanin alpha subunit
L3: C-phycocyanin beta subunit
M3: C-phycocyanin beta subunit
N3: C-phycocyanin alpha subunit
O3: C-phycocyanin beta subunit
P3: C-phycocyanin beta subunit
Q3: C-phycocyanin beta subunit
R3: C-phycocyanin alpha subunit
S3: C-phycocyanin alpha subunit
T3: C-phycocyanin alpha subunit
U3: C-phycocyanin alpha subunit
V3: C-phycocyanin beta subunit
W3: C-phycocyanin alpha subunit
X3: C-phycocyanin beta subunit
Y3: Phycobilisome rod linker polypeptide
Z3: Phycobilisome rod linker polypeptide
a3: C-phycocyanin beta subunit
B4: C-phycocyanin alpha subunit
C4: C-phycocyanin beta subunit
D4: C-phycocyanin beta subunit
E4: C-phycocyanin beta subunit
F4: C-phycocyanin alpha subunit
G4: C-phycocyanin alpha subunit
H4: C-phycocyanin alpha subunit
I4: C-phycocyanin alpha subunit
J4: C-phycocyanin beta subunit
K4: C-phycocyanin alpha subunit
L4: C-phycocyanin beta subunit
M4: C-phycocyanin beta subunit
N4: C-phycocyanin alpha subunit
O4: C-phycocyanin beta subunit
P4: C-phycocyanin beta subunit
Q4: C-phycocyanin beta subunit
R4: C-phycocyanin alpha subunit
S4: C-phycocyanin alpha subunit
T4: C-phycocyanin alpha subunit
U4: C-phycocyanin alpha subunit
V4: C-phycocyanin beta subunit
W4: C-phycocyanin alpha subunit
X4: C-phycocyanin beta subunit
Y4: Phycobilisome rod linker polypeptide
Z4: Phycobilisome rod linker polypeptide
a4: C-phycocyanin beta subunit
B5: C-phycocyanin alpha subunit
C5: C-phycocyanin beta subunit
D5: C-phycocyanin beta subunit
E5: C-phycocyanin beta subunit
F5: C-phycocyanin alpha subunit
G5: C-phycocyanin alpha subunit
H5: C-phycocyanin alpha subunit
I5: C-phycocyanin alpha subunit
J5: C-phycocyanin beta subunit
K5: C-phycocyanin alpha subunit
L5: C-phycocyanin beta subunit
M5: C-phycocyanin beta subunit
N5: C-phycocyanin alpha subunit
O5: C-phycocyanin beta subunit
P5: C-phycocyanin beta subunit
Q5: C-phycocyanin beta subunit
R5: C-phycocyanin alpha subunit
S5: C-phycocyanin alpha subunit
T5: C-phycocyanin alpha subunit
U5: C-phycocyanin alpha subunit
V5: C-phycocyanin beta subunit
W5: C-phycocyanin alpha subunit
X5: C-phycocyanin beta subunit
Y5: Phycobilisome rod linker polypeptide
Z5: Phycobilisome rod linker polypeptide
a5: C-phycocyanin beta subunit
A6: Phycobilisome rod-core linker polypeptide
B6: C-phycocyanin alpha subunit
C6: C-phycocyanin beta subunit
D6: C-phycocyanin beta subunit
E6: C-phycocyanin beta subunit
F6: C-phycocyanin alpha subunit
G6: C-phycocyanin alpha subunit
H6: C-phycocyanin alpha subunit
I6: C-phycocyanin alpha subunit
J6: C-phycocyanin beta subunit
K6: C-phycocyanin alpha subunit
L6: C-phycocyanin beta subunit
M6: C-phycocyanin beta subunit
N6: C-phycocyanin alpha subunit
O6: C-phycocyanin beta subunit
P6: C-phycocyanin beta subunit
Q6: C-phycocyanin beta subunit
R6: C-phycocyanin alpha subunit
S6: C-phycocyanin alpha subunit
T6: C-phycocyanin alpha subunit
U6: C-phycocyanin alpha subunit
V6: C-phycocyanin beta subunit
W6: C-phycocyanin alpha subunit
X6: C-phycocyanin beta subunit
Y6: Phycobilisome rod linker polypeptide
Z6: Phycobilisome rod linker polypeptide
a6: C-phycocyanin beta subunit
B7: C-phycocyanin alpha subunit
C7: C-phycocyanin beta subunit
D7: C-phycocyanin beta subunit
E7: C-phycocyanin beta subunit
F7: C-phycocyanin alpha subunit
G7: C-phycocyanin alpha subunit
H7: C-phycocyanin alpha subunit
I7: C-phycocyanin alpha subunit
J7: C-phycocyanin beta subunit
K7: C-phycocyanin alpha subunit
L7: C-phycocyanin beta subunit
M7: C-phycocyanin beta subunit
N7: C-phycocyanin alpha subunit
O7: C-phycocyanin beta subunit
P7: C-phycocyanin beta subunit
Q7: C-phycocyanin beta subunit
R7: C-phycocyanin alpha subunit
S7: C-phycocyanin alpha subunit
T7: C-phycocyanin alpha subunit
U7: C-phycocyanin alpha subunit
V7: C-phycocyanin beta subunit
W7: C-phycocyanin alpha subunit
X7: C-phycocyanin beta subunit
Y7: Phycobilisome rod linker polypeptide
Z7: Phycobilisome rod linker polypeptide
a7: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,271,174468
Polymers4,122,823216
Non-polymers148,351252
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Phycobilisome ... , 4 types, 22 molecules A122324252A6Y1Y3Y4Y5Y6Y7Z1Z3Z4Z5Z6Z702Y2Z2z2

#1: Protein
Phycobilisome rod-core linker polypeptide


Mass: 28372.934 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31LK9
#4: Protein
Phycobilisome rod linker polypeptide


Mass: 30420.775 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31PE0
#5: Protein
Phycobilisome rod linker polypeptide


Mass: 31734.639 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31PD9
#6: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7821.201 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RG2

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C-phycocyanin ... , 2 types, 144 molecules B1F1G1H1I1K1N1R1S1T1U1W1B3F3G3H3I3K3N3R3S3T3U3W3B4F4G4H4I4K4...

#2: Protein ...
C-phycocyanin alpha subunit


Mass: 17303.238 Da / Num. of mol.: 72 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: P13530
#3: Protein ...
C-phycocyanin beta subunit


Mass: 18287.713 Da / Num. of mol.: 72 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: P06539

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Protein , 2 types, 4 molecules 12b2N2o2

#7: Protein ApcG


Mass: 11365.804 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RM8
#10: Protein Phycobiliprotein ApcE


Mass: 78910.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RF9

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Allophycocyanin, beta ... , 2 types, 24 molecules A2B2C2F2K2L2M2O2T2V2X2a2c2d2g2l2m2n2p2u2w2y2P2q2

#8: Protein ...
Allophycocyanin, beta subunit


Mass: 17408.725 Da / Num. of mol.: 22 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RG1
#11: Protein Allophycocyanin, beta subunit / Phycobilisome core component


Mass: 18590.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ApcF
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: O50209

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Allophycocyanin ... , 2 types, 22 molecules D2E2G2H2I2J2Q2R2U2W2e2f2h2i2j2k2r2s2v2x2S2t2

#9: Protein
Allophycocyanin alpha chain


Mass: 17439.717 Da / Num. of mol.: 20 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RG0
#12: Protein Allophycocyanin alpha-B chain


Mass: 18149.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31RP7

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Non-polymers , 1 types, 252 molecules

#13: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 252 / Source method: obtained synthetically / Formula: C33H40N4O6

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: the major light-harvesting complexes Phycobilisomes (PBSs)
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1UCSF ChimeraXparticle selection
2PHENIX1.19.2_4158model refinement
13UCSF ChimeraX3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: OTHER / Num. of particles: 258722 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003292081
ELECTRON MICROSCOPYf_angle_d0.617397232
ELECTRON MICROSCOPYf_dihedral_angle_d11.402107019
ELECTRON MICROSCOPYf_chiral_restr0.03544636
ELECTRON MICROSCOPYf_plane_restr0.00351296

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