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- PDB-9k9w: structure of bundle-shaped PBS with short rod -

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Basic information

Entry
Database: PDB / ID: 9k9w
Titlestructure of bundle-shaped PBS with short rod
Components
  • (Allophycocyanin ...) x 2
  • (Phycocyanin-associated rod linker ...) x 2
  • CpcD protein
  • Glr1262 protein
  • Glr2806 protein
  • Phycobiliprotein ApcE
  • Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Phycocyanin alpha chain
  • Phycocyanin beta chain
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 / Phycobilisome linker protein / 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 ...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. / 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 / Phycocyanin beta chain / Phycocyanin alpha chain / Phycocyanin-associated rod linker protein / Glr2806 protein / CpcD protein / Glr1262 protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Allophycocyanin alpha subunit ...PHYCOCYANOBILIN / Phycocyanin beta chain / Phycocyanin alpha chain / Phycocyanin-associated rod linker protein / Glr2806 protein / CpcD protein / Glr1262 protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Allophycocyanin alpha subunit / Phycobiliprotein ApcE / Phycocyanin-associated rod linker protein
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSui, S.-F. / Ma, J. / You, X. / Sun, S.
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
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allophycocyanin beta subunit
Z: Allophycocyanin beta subunit
AA: Phycocyanin alpha chain
BA: Phycocyanin beta chain
CA: Phycocyanin alpha chain
DA: Phycocyanin beta chain
EA: Phycocyanin alpha chain
FA: Phycocyanin beta chain
GA: Phycocyanin alpha chain
HA: Phycocyanin beta chain
IA: Phycocyanin alpha chain
JA: Phycocyanin beta chain
KA: Phycocyanin alpha chain
LA: Phycocyanin beta chain
MA: Phycocyanin-associated rod linker protein
NA: Phycocyanin-associated rod linker protein
OA: Phycocyanin alpha chain
PA: Phycocyanin beta chain
QA: Phycocyanin alpha chain
RA: Phycocyanin beta chain
SA: Phycocyanin alpha chain
TA: Phycocyanin beta chain
UA: Phycocyanin alpha chain
VA: Phycocyanin beta chain
WA: Phycocyanin alpha chain
XA: Phycocyanin beta chain
YA: Phycocyanin alpha chain
ZA: Phycocyanin beta chain
O1: Phycocyanin alpha chain
P1: Phycocyanin beta chain
Q1: Phycocyanin alpha chain
R1: Phycocyanin beta chain
S1: Phycocyanin alpha chain
A1: Phycocyanin alpha chain
G3: Phycocyanin alpha chain
H3: Phycocyanin beta chain
I3: Phycocyanin alpha chain
J3: Phycocyanin beta chain
K3: Phycocyanin alpha chain
G2: Phycocyanin alpha chain
H2: Phycocyanin beta chain
I2: Phycocyanin alpha chain
J2: Phycocyanin beta chain
K2: Phycocyanin alpha chain
L2: Phycocyanin beta chain
M2: Glr2806 protein
N2: CpcD protein
A3: Phycocyanin alpha chain
B3: Phycocyanin beta chain
C3: Phycocyanin alpha chain
D3: Phycocyanin beta chain
E3: Phycocyanin alpha chain
F3: Phycocyanin beta chain
Z3: Phycocyanin beta chain
A4: Phycocyanin alpha chain
B4: Phycocyanin beta chain
C4: Phycocyanin alpha chain
D4: Phycocyanin beta chain
L3: Phycocyanin beta chain
M3: Phycocyanin-associated rod linker protein
N3: Phycocyanin-associated rod linker protein
O3: Phycocyanin alpha chain
P3: Phycocyanin beta chain
Q3: Phycocyanin alpha chain
R3: Phycocyanin beta chain
S3: Phycocyanin alpha chain
T3: Phycocyanin beta chain
U3: Phycocyanin alpha chain
V3: Phycocyanin beta chain
W3: Phycocyanin alpha chain
X3: Phycocyanin beta chain
Y3: Phycocyanin alpha chain
B1: Phycocyanin beta chain
S4: Phycocyanin beta chain
T4: Phycocyanin alpha chain
U4: Phycocyanin beta chain
V4: Phycocyanin alpha chain
W4: Phycocyanin beta chain
E4: Phycocyanin alpha chain
F4: Phycocyanin beta chain
G4: Phycocyanin alpha chain
H4: Phycocyanin beta chain
I4: Phycocyanin alpha chain
J4: Phycocyanin beta chain
K4: Phycocyanin alpha chain
L4: Phycocyanin beta chain
M4: Phycocyanin-associated rod linker protein
N4: Phycocyanin alpha chain
O4: Phycocyanin beta chain
P4: Phycocyanin alpha chain
Q4: Phycocyanin beta chain
R4: Phycocyanin alpha chain
K5: Allophycocyanin alpha subunit
L5: Allophycocyanin beta subunit
M5: Allophycocyanin alpha subunit
N5: Allophycocyanin beta subunit
O5: Allophycocyanin alpha subunit
X4: Phycocyanin alpha chain
Y4: Phycocyanin beta chain
Z4: Phycocyanin-associated rod linker protein
A5: Allophycocyanin alpha subunit
B5: Allophycocyanin beta subunit
C5: Allophycocyanin alpha subunit
D5: Allophycocyanin beta subunit
E5: Allophycocyanin alpha subunit
F5: Allophycocyanin beta subunit
G5: Allophycocyanin alpha subunit
H5: Allophycocyanin beta subunit
I5: Allophycocyanin alpha subunit
J5: Allophycocyanin beta subunit
C1: Phycocyanin alpha chain
c5: Allophycocyanin alpha subunit
d5: Allophycocyanin beta subunit
e5: Allophycocyanin alpha subunit
f5: Allophycocyanin beta subunit
P5: Allophycocyanin beta subunit
Q5: Allophycocyanin alpha subunit
R5: Allophycocyanin beta subunit
S5: Allophycocyanin alpha subunit
T5: Allophycocyanin beta subunit
U5: Allophycocyanin alpha subunit
V5: Allophycocyanin beta subunit
W5: Allophycocyanin alpha subunit
X5: Allophycocyanin beta subunit
Y5: Allophycocyanin alpha subunit
Z5: Allophycocyanin beta subunit
a5: Allophycocyanin alpha subunit
b5: Allophycocyanin beta subunit
J6: Phycocyanin beta chain
K6: Phycocyanin alpha chain
L6: Phycocyanin beta chain
M6: Glr2806 protein
N6: CpcD protein
A7: Allophycocyanin alpha subunit
z5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
i5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
j5: Phycobiliprotein ApcE
k5: Phycobiliprotein ApcE
A6: Phycocyanin alpha chain
B6: Phycocyanin beta chain
C6: Phycocyanin alpha chain
D6: Phycocyanin beta chain
E6: Phycocyanin alpha chain
F6: Phycocyanin beta chain
G6: Phycocyanin alpha chain
H6: Phycocyanin beta chain
I6: Phycocyanin alpha chain
D1: Phycocyanin beta chain
O7: Allophycocyanin alpha subunit
P7: Allophycocyanin beta subunit
Q7: Allophycocyanin alpha subunit
R7: Allophycocyanin beta subunit
S7: Allophycocyanin alpha subunit
B7: Allophycocyanin beta subunit
C7: Allophycocyanin alpha subunit
D7: Allophycocyanin beta subunit
E7: Allophycocyanin alpha subunit
F7: Allophycocyanin beta subunit
G7: Allophycocyanin alpha subunit
H7: Allophycocyanin beta subunit
I7: Allophycocyanin alpha subunit
J7: Allophycocyanin beta subunit
K7: Allophycocyanin alpha subunit
L7: Allophycocyanin beta subunit
M7: Allophycocyanin alpha subunit
N7: Allophycocyanin beta subunit
g7: Allophycocyanin alpha subunit
h7: Allophycocyanin beta subunit
i7: Allophycocyanin alpha subunit
j7: Allophycocyanin beta subunit
k7: Allophycocyanin alpha subunit
T7: Allophycocyanin beta subunit
U7: Allophycocyanin alpha subunit
V7: Allophycocyanin beta subunit
W7: Allophycocyanin alpha subunit
X7: Allophycocyanin beta subunit
Y7: Allophycocyanin alpha subunit
Z7: Allophycocyanin beta subunit
a7: Allophycocyanin alpha subunit
b7: Allophycocyanin beta subunit
c7: Allophycocyanin alpha subunit
d7: Allophycocyanin beta subunit
e7: Allophycocyanin alpha subunit
f7: Allophycocyanin beta subunit
E1: Phycocyanin alpha chain
A8: Phycocyanin alpha chain
B8: Phycocyanin beta chain
C8: Phycocyanin alpha chain
D8: Phycocyanin beta chain
E8: Phycocyanin alpha chain
l7: Allophycocyanin beta subunit
m7: Allophycocyanin alpha subunit
n7: Allophycocyanin beta subunit
o7: Allophycocyanin alpha subunit
p7: Allophycocyanin beta subunit
q7: Allophycocyanin alpha subunit
r7: Allophycocyanin beta subunit
s7: Allophycocyanin alpha subunit
t7: Allophycocyanin beta subunit
u7: Allophycocyanin alpha subunit
v7: Allophycocyanin beta subunit
z7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
w7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
x7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
y7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
T8: Phycocyanin alpha chain
U8: Phycocyanin beta chain
V8: Phycocyanin alpha chain
W8: Phycocyanin beta chain
X8: Phycocyanin alpha chain
F8: Phycocyanin beta chain
G8: Phycocyanin alpha chain
H8: Phycocyanin beta chain
I8: Phycocyanin alpha chain
J8: Phycocyanin beta chain
K8: Phycocyanin alpha chain
L8: Phycocyanin beta chain
M8: Phycocyanin-associated rod linker protein
N8: Phycocyanin alpha chain
O8: Phycocyanin beta chain
P8: Phycocyanin alpha chain
Q8: Phycocyanin beta chain
R8: Phycocyanin alpha chain
S8: Phycocyanin beta chain
F1: Phycocyanin beta chain
L9: Phycocyanin beta chain
M9: Phycocyanin-associated rod linker protein
N9: Phycocyanin-associated rod linker protein
O9: Phycocyanin alpha chain
P9: Phycocyanin beta chain
Q9: Phycocyanin alpha chain
Y8: Phycocyanin beta chain
Z8: Phycocyanin-associated rod linker protein
A9: Phycocyanin alpha chain
B9: Phycocyanin beta chain
C9: Phycocyanin alpha chain
D9: Phycocyanin beta chain
E9: Phycocyanin alpha chain
F9: Phycocyanin beta chain
G9: Phycocyanin alpha chain
H9: Phycocyanin beta chain
I9: Phycocyanin alpha chain
J9: Phycocyanin beta chain
K9: Phycocyanin alpha chain
R9: Phycocyanin beta chain
S9: Phycocyanin alpha chain
T9: Phycocyanin beta chain
U9: Phycocyanin alpha chain
V9: Phycocyanin beta chain
W9: Phycocyanin alpha chain
X9: Phycocyanin beta chain
Y9: Phycocyanin alpha chain
Z9: Phycocyanin beta chain
G1: Phycocyanin alpha chain
a9: Glr1262 protein
aA: Glr1262 protein
H1: Phycocyanin beta chain
I1: Phycocyanin alpha chain
J1: Phycocyanin beta chain
K1: Phycocyanin alpha chain
L1: Phycocyanin beta chain
M1: Phycocyanin-associated rod linker protein
N1: Phycocyanin-associated rod linker protein
T1: Phycocyanin beta chain
U1: Phycocyanin alpha chain
V1: Phycocyanin beta chain
W1: Phycocyanin alpha chain
X1: Phycocyanin beta chain
Y1: Phycocyanin alpha chain
Z1: Phycocyanin beta chain
A2: Phycocyanin alpha chain
B2: Phycocyanin beta chain
C2: Phycocyanin alpha chain
D2: Phycocyanin beta chain
E2: Phycocyanin alpha chain
F2: Phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,701,551612
Polymers5,503,749276
Non-polymers197,801336
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Allophycocyanin ... , 2 types, 82 molecules AZL5N5B5D5F5H5J5d5f5P5R5T5V5X5Z5b5P7R7B7D7F7H7J7L7N7h7j7T7...

#1: Protein ...
Allophycocyanin beta subunit


Mass: 17241.664 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL79
#8: Protein ...
Allophycocyanin alpha subunit


Mass: 17539.039 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL80

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Protein , 7 types, 182 molecules AACAEAGAIAKAOAQASAUAWAYAO1Q1S1A1G3I3K3G2I2K2A3C3E3A4C4O3Q3S3...

#2: Protein ...
Phycocyanin alpha chain


Mass: 17679.852 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7M7F7
#3: Protein ...
Phycocyanin beta chain


Mass: 18478.953 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7M7C7
#6: Protein Glr2806 protein


Mass: 81544.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NGT2
#7: Protein CpcD protein


Mass: 7776.872 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL59
#9: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7633.809 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL78
#10: 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
#11: Protein Glr1262 protein


Mass: 92127.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL64

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Phycocyanin-associated rod linker ... , 2 types, 12 molecules MAM3M4M8M9M1NAN3Z4N9Z8N1

#4: Protein
Phycocyanin-associated rod linker protein


Mass: 30913.822 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: There is no expression tag in the Phycocyanin-associated rod linker proteins (MA, M3, M4, M8, M9 and M1) or the Phycocyanin-associated rod linker proteins (NA, N3, Z4, N9, Z8 and N1). We ...Details: There is no expression tag in the Phycocyanin-associated rod linker proteins (MA, M3, M4, M8, M9 and M1) or the Phycocyanin-associated rod linker proteins (NA, N3, Z4, N9, Z8 and N1). We align all amino acids by their electron density map.
Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NGF2
#5: Protein
Phycocyanin-associated rod linker protein


Mass: 31085.066 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NM19

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Non-polymers , 1 types, 336 molecules

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


Mass: 588.694 Da / Num. of mol.: 336 / 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: #6, #5 / Source: NATURAL
Molecular weightValue: 14700 kDa/nm / Experimental value: NO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
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 material: COPPER / Grid mesh size: 300 divisions/in. / Grid 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 K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6438
EM imaging opticsEnergyfilter name: GIF Quantum ER / Energyfilter slit width: 20 eV
Spherical aberration corrector: Spherical aberration (Cs) corrector
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
1RELION3.1betaparticle selection
4CTFFIND4.15CTF correction
7UCSF Chimeramodel fitting
9RELION3.1betainitial Euler assignment
10RELION3.1betafinal Euler assignment
11RELION3.1betaclassification
12RELION3.1beta3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1042622
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 389430 / Symmetry type: POINT
Atomic model buildingB value: 62.05 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0,99
Atomic model buildingPDB-ID: 6KGX

6kgx


Accession code: 6KGX / Source name: PDB / Type: experimental model

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