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- PDB-9wd5: Cryo-EM structure of PSI-CpcL -

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Basic information

Entry
Database: PDB / ID: 9wd5
TitleCryo-EM structure of PSI-CpcL
Components
  • (Photosystem I ...) x 12
  • Photosystem I-associated linker protein CpcL
KeywordsPHOTOSYNTHESIS / Photosystem I
Function / homology
Function and homology information


photosystem I reaction center / phycobilisome / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / phycobilisome / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I iron-sulfur center / Photosystem I-associated linker protein CpcL ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I iron-sulfur center / Photosystem I-associated linker protein CpcL / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsMao, Z.Y. / Li, Z.H. / Han, G.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insight of a photosystem I-CpcL-phycobilisome supercomplex from a cyanobacterium sp. PCC 7120.
Authors: Zhiyuan Mao / Zhenhua Li / Xingyue Li / Liangliang Shen / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / Guangye Han /
Abstract: Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light ...Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light energy to photosystem II (PSII) and photosystem I (PSI) in cyanobacteria and eukaryotic red algae. In cyanobacteria, a rod-type PBS that does not have a core is specifically connected to PSI by a linker protein CpcL to form a PSI-CpcL-PBS supercomplex. However, the mechanism of CpcL-PBS association to PSI remains unclear. Here, we report the cryoelectron microscopic structures of PSI-CpcL-PBS at 2.98 Å and CpcL-PBS at 2.93 Å resolution from a cyanobacterium sp. PCC 7120, respectively. CpcL-PBS is located on the stromal side of a PSI tetramer and exhibits a structure of three-layered PBS consisting of four linkers (CpcL, CpcC1, CpcC2, PecC) and 18 pairs of phycocyanin αβ monomers. The C-terminal transmembrane helix of CpcL inserts to the membrane and interacts with PsaA, PsaB, and PsaM of PSI at an interface I between two PSI monomers, enabling the formation of the PSI-CpcL-PBS supercomplex. The exact structure of protein subunits and arrangement of bilin and chlorophyll pigments are revealed, which provide a structural basis for the assembly of PSI-CpcL-PBS and possible excitation energy transfer pathways from antennas to PSI within this supercomplex, shedding light on the organization and attachment of CpcL-PBS in cyanobacterial thylakoids.
History
DepositionAug 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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

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Assembly

Deposited unit
1: Photosystem I-associated linker protein CpcL
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I 4.8 kDa protein
N: Photosystem I P700 chlorophyll a apoprotein A2 1
P: Photosystem I iron-sulfur center
Q: Photosystem I reaction center subunit II
R: Photosystem I reaction center subunit IV
S: Photosystem I reaction center subunit III
T: Photosystem I reaction center subunit IX
U: Photosystem I reaction center subunit PsaK 1
V: Photosystem I reaction center subunit VIII
W: Photosystem I reaction center subunit XI
Y: Photosystem I reaction center subunit XII
g: Photosystem I P700 chlorophyll a apoprotein A1
h: Photosystem I 4.8 kDa protein
n: Photosystem I P700 chlorophyll a apoprotein A2 1
p: Photosystem I iron-sulfur center
q: Photosystem I reaction center subunit II
r: Photosystem I reaction center subunit IV
s: Photosystem I reaction center subunit III
t: Photosystem I reaction center subunit IX
u: Photosystem I reaction center subunit PsaK 1
v: Photosystem I reaction center subunit VIII
w: Photosystem I reaction center subunit XI
y: Photosystem I reaction center subunit XII
A: Photosystem I P700 chlorophyll a apoprotein A1
X: Photosystem I 4.8 kDa protein
B: Photosystem I P700 chlorophyll a apoprotein A2 1
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 1
I: Photosystem I reaction center subunit VIII
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
a: Photosystem I P700 chlorophyll a apoprotein A1
x: Photosystem I 4.8 kDa protein
b: Photosystem I P700 chlorophyll a apoprotein A2 1
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK 1
i: Photosystem I reaction center subunit VIII
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,493,561567
Polymers1,077,05849
Non-polymers416,503518
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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Protein , 1 types, 1 molecules 1

#1: Protein Photosystem I-associated linker protein CpcL / L-RC 27.2 / Phycobilisome rod-core linker polypeptide CpcG3


Mass: 27232.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P29988

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Photosystem I ... , 12 types, 48 molecules GgAaHhXxNnBbPpCcQqDdRrEeSsFfTt...

#2: Protein
Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83289.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58576, photosystem I
#3: Protein/peptide
Photosystem I 4.8 kDa protein


Mass: 4872.792 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58566
#4: Protein
Photosystem I P700 chlorophyll a apoprotein A2 1 / PsaB 1


Mass: 83457.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58565, photosystem I
#5: Protein
Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.206 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P0A410, photosystem I
#6: Protein
Photosystem I reaction center subunit II


Mass: 15176.240 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58573
#7: Protein
Photosystem I reaction center subunit IV


Mass: 7897.051 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58575
#8: Protein
Photosystem I reaction center subunit III / PSI-F


Mass: 17850.568 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58564
#9: Protein/peptide
Photosystem I reaction center subunit IX


Mass: 5499.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58568
#10: Protein
Photosystem I reaction center subunit PsaK 1 / Photosystem I subunit X 1


Mass: 8852.457 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58583
#11: Protein/peptide
Photosystem I reaction center subunit VIII


Mass: 5066.925 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58560
#12: Protein
Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 18130.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P58577
#13: Protein/peptide
Photosystem I reaction center subunit XII / PSI-M


Mass: 3538.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: Q8YNB0

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Non-polymers , 8 types, 518 molecules

#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 376 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical
ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: PSI-CpcL / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120345 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004104565
ELECTRON MICROSCOPYf_angle_d0.663147603
ELECTRON MICROSCOPYf_dihedral_angle_d18.82616833
ELECTRON MICROSCOPYf_chiral_restr0.03912898
ELECTRON MICROSCOPYf_plane_restr0.00419569

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