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- PDB-9m3j: structure of bundle-shaped PBS with both long rod and (ApcA2B3Apc... -

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Basic information

Entry
Database: PDB / ID: 9m3j
Titlestructure of bundle-shaped PBS with both long rod and (ApcA2B3ApcD) trimer
Components
  • (Allophycocyanin ...) x 2
  • Allophycocyanin-B
  • Phycobiliprotein ApcE
  • Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
KeywordsPHOTOSYNTHESIS / phycobilisome / light-harvesting complex
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / 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 / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsMa, J. / Sui, S.-F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670745 China
National Natural Science Foundation of China (NSFC)31861143048 China
CitationJournal: Nat Commun / Year: 2025
Title: Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus.
Authors: Jianfei Ma / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, ...Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solve the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures reveal two unique linker proteins, L and L, that play a key role in the PBS architecture. Analysis of the bilin arrangement indicates that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovers a distinct mode of adaption to increased light intensity wherein the ApcA-ApcB-ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus L. This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.
History
DepositionMar 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Allophycocyanin alpha subunit
B1: Allophycocyanin beta subunit
C1: Allophycocyanin alpha subunit
D1: Allophycocyanin beta subunit
F1: Allophycocyanin beta subunit
E1: Allophycocyanin alpha subunit
G1: Allophycocyanin beta subunit
H1: Allophycocyanin alpha subunit
I1: Allophycocyanin beta subunit
J1: Allophycocyanin beta subunit
K1: Allophycocyanin-B
L1: Allophycocyanin-B
z1: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
M1: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
A2: Allophycocyanin alpha subunit
B2: Allophycocyanin beta subunit
C2: Allophycocyanin alpha subunit
D2: Allophycocyanin beta subunit
E2: Allophycocyanin alpha subunit
F2: Allophycocyanin beta subunit
G2: Allophycocyanin alpha subunit
H2: Allophycocyanin beta subunit
I2: Allophycocyanin alpha subunit
J2: Allophycocyanin beta subunit
K2: Allophycocyanin alpha subunit
L2: Allophycocyanin beta subunit
M2: Allophycocyanin alpha subunit
N2: Allophycocyanin beta subunit
O2: Allophycocyanin alpha subunit
P2: Allophycocyanin beta subunit
Q2: Allophycocyanin alpha subunit
R2: Allophycocyanin beta subunit
S2: Allophycocyanin alpha subunit
T2: Allophycocyanin beta subunit
U2: Allophycocyanin alpha subunit
V2: Allophycocyanin beta subunit
W2: Allophycocyanin alpha subunit
X2: Allophycocyanin beta subunit
Y2: Allophycocyanin alpha subunit
Z2: Allophycocyanin beta subunit
a2: Allophycocyanin alpha subunit
b2: Allophycocyanin beta subunit
c2: Allophycocyanin alpha subunit
d2: Allophycocyanin beta subunit
e2: Allophycocyanin alpha subunit
f2: Allophycocyanin beta subunit
g2: Allophycocyanin alpha subunit
h2: Allophycocyanin beta subunit
i2: Allophycocyanin alpha subunit
j2: Allophycocyanin beta subunit
k2: Allophycocyanin alpha subunit
l2: Allophycocyanin beta subunit
m2: Allophycocyanin alpha subunit
n2: Allophycocyanin beta subunit
o2: Allophycocyanin alpha subunit
p2: Allophycocyanin beta subunit
q2: Allophycocyanin alpha subunit
r2: Allophycocyanin beta subunit
s2: Allophycocyanin alpha subunit
t2: Allophycocyanin beta subunit
u2: Allophycocyanin alpha subunit
v2: Allophycocyanin beta subunit
z2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
w2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
x2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
y2: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
A3: Allophycocyanin alpha subunit
B3: Allophycocyanin beta subunit
C3: Allophycocyanin alpha subunit
D3: Allophycocyanin beta subunit
E3: Allophycocyanin alpha subunit
F3: Allophycocyanin beta subunit
G3: Allophycocyanin alpha subunit
H3: Allophycocyanin beta subunit
I3: Allophycocyanin alpha subunit
J3: Allophycocyanin beta subunit
K3: Allophycocyanin alpha subunit
L3: Allophycocyanin beta subunit
M3: Allophycocyanin alpha subunit
N3: Allophycocyanin beta subunit
O3: Allophycocyanin alpha subunit
P3: Allophycocyanin beta subunit
Q3: Allophycocyanin alpha subunit
R3: Allophycocyanin beta subunit
S3: Allophycocyanin alpha subunit
T3: Allophycocyanin beta subunit
U3: Allophycocyanin alpha subunit
V3: Allophycocyanin beta subunit
W3: Allophycocyanin alpha subunit
X3: Allophycocyanin beta subunit
Y3: Allophycocyanin alpha subunit
Z3: Allophycocyanin beta subunit
a3: Allophycocyanin alpha subunit
b3: Allophycocyanin beta subunit
c3: Allophycocyanin alpha subunit
d3: Allophycocyanin beta subunit
e3: Allophycocyanin alpha subunit
f3: Allophycocyanin beta subunit
g3: Allophycocyanin beta subunit
z3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
i3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
j3: Phycobiliprotein ApcE
k3: Phycobiliprotein ApcE
h3: Allophycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,014,058200
Polymers1,957,544104
Non-polymers56,51596
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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Allophycocyanin ... , 2 types, 92 molecules A1C1E1H1A2C2E2G2I2K2M2O2Q2S2U2W2Y2a2c2e2g2i2k2m2o2q2s2u2A3C3...

#1: Protein ...
Allophycocyanin alpha subunit


Mass: 17539.039 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria)
#2: Protein ...
Allophycocyanin beta subunit


Mass: 17241.664 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL79

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Protein , 3 types, 12 molecules K1L1z1M1z2w2x2y2z3i3j3k3

#3: Protein Allophycocyanin-B


Mass: 18050.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria)
#4: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7765.004 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL78
#5: Protein Phycobiliprotein ApcE


Mass: 130002.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL81

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Non-polymers , 1 types, 96 molecules

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


Mass: 588.694 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: phycobilisome / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 7 MDa / Experimental value: YES
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria) / Strain: PCC 7421
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
10.75 mol/Ldisodium hydrogen phosphateNa2HPO41
20.75 mol/LMonobasic Potassium PhosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 18 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 2300 nm / Cs: 0.001 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingAverage exposure time: 8.2 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10942
EM imaging opticsEnergyfilter name: GIF Quantum ER / Energyfilter slit width: 20 eV
Spherical aberration corrector: Spherical aberration (Cs) corrector
Image scansWidth: 5760 / Height: 4092 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.0.2particle selection
4CTFFIND4.15CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARC4.0.2initial Euler assignment
11cryoSPARC4.0.2final Euler assignment
12cryoSPARC4.0.2classification
13cryoSPARC4.0.23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 605750
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192814 / Symmetry type: POINT
Atomic model buildingB value: 62.05 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0,99
Atomic model buildingSource name: AlphaFold / Type: in silico model

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