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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: Ma, J. / You, X. / Sun, S. / Sui, S.F.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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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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