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- PDB-9lzj: The PSI3-IsiA43 complex with a closed double ring of IsiA protein... -

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Basic information

Entry
Database: PDB / ID: 9lzj
TitleThe PSI3-IsiA43 complex with a closed double ring of IsiA proteins bound to a trimeric PSI core
Components
  • (Photosystem I ...) x 12
  • Iron stress-induced chlorophyll-binding protein
KeywordsPHOTOSYNTHESIS / Photosystem-antenna Complex
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosynthetic electron transport chain / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / 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 antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 PsaJ, reaction centre subunit IX superfamily / 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 / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / 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 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 ...BETA-CAROTENE / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Iron stress-induced chlorophyll-binding protein / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSi, L. / Cao, P. / Li, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930064, 32070259 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the assembly and energy transfer between the cyanobacterial PSI core and the double-layered IsiA proteins.
Authors: Long Si / Yingyue Zhang / Xiaodong Su / Xuelin Zhao / Xiaomin An / Lu-Ning Liu / Peng Cao / Mei Li /
Abstract: Iron-limitation is a common stress factor in natural environments. To survive under iron-starved conditions, cyanobacteria overexpress iron stress-induced protein A (IsiA), which is crucial for light- ...Iron-limitation is a common stress factor in natural environments. To survive under iron-starved conditions, cyanobacteria overexpress iron stress-induced protein A (IsiA), which is crucial for light-harvesting and photoprotection. Multiple IsiA proteins form a single- or double-layered architecture encircling the photosystem I (PSI) core, forming various PSI-IsiA supercomplexes. The assembly and energy transfer mechanisms of double-layered PSI-IsiA supercomplexes remain unelucidated. Here, we present high-resolution structures of two PSI-IsiA supercomplexes isolated from the cyanobacterium Thermosynechococcus elongatus BP-1 cultured under iron-starved conditions. The PSI-IsiA complex contains a trimeric PSI core surrounded by 43 IsiA subunits assembled into a closed double-ring. The PSI-IsiA complex contains 13 IsiA proteins arranged in a double-layered architecture attached to the monomeric PSI core. Atomic force microscopy demonstrates the presence and distribution of different PSI-IsiA complexes within native thylakoid membranes isolated from iron-starved cells. Our findings provide insights into the structural variability and adaptive mechanisms of PSI-IsiA complexes.
History
DepositionFeb 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 2.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
aA: Photosystem I P700 chlorophyll a apoprotein A1
aB: Photosystem I P700 chlorophyll a apoprotein A2
aC: Photosystem I iron-sulfur center
aD: Photosystem I reaction center subunit II
aE: Photosystem I reaction center subunit IV
aF: Photosystem I reaction center subunit III
aI: Photosystem I reaction center subunit VIII
aJ: Photosystem I reaction center subunit IX
aK: Photosystem I reaction center subunit PsaK
aL: Photosystem I reaction center subunit XI
aM: Photosystem I reaction center subunit XII
aX: Photosystem I 4.8K protein
a1: Iron stress-induced chlorophyll-binding protein
a2: Iron stress-induced chlorophyll-binding protein
a3: Iron stress-induced chlorophyll-binding protein
a4: Iron stress-induced chlorophyll-binding protein
a5: Iron stress-induced chlorophyll-binding protein
a6: Iron stress-induced chlorophyll-binding protein
bA: Photosystem I P700 chlorophyll a apoprotein A1
bB: Photosystem I P700 chlorophyll a apoprotein A2
bC: Photosystem I iron-sulfur center
bD: Photosystem I reaction center subunit II
bE: Photosystem I reaction center subunit IV
bF: Photosystem I reaction center subunit III
bI: Photosystem I reaction center subunit VIII
bJ: Photosystem I reaction center subunit IX
bK: Photosystem I reaction center subunit PsaK
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
bX: Photosystem I 4.8K protein
b1: Iron stress-induced chlorophyll-binding protein
b2: Iron stress-induced chlorophyll-binding protein
b3: Iron stress-induced chlorophyll-binding protein
b4: Iron stress-induced chlorophyll-binding protein
b5: Iron stress-induced chlorophyll-binding protein
b6: Iron stress-induced chlorophyll-binding protein
cA: Photosystem I P700 chlorophyll a apoprotein A1
cB: Photosystem I P700 chlorophyll a apoprotein A2
cC: Photosystem I iron-sulfur center
cD: Photosystem I reaction center subunit II
cE: Photosystem I reaction center subunit IV
cF: Photosystem I reaction center subunit III
cI: Photosystem I reaction center subunit VIII
cJ: Photosystem I reaction center subunit IX
cK: Photosystem I reaction center subunit PsaK
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
cX: Photosystem I 4.8K protein
c1: Iron stress-induced chlorophyll-binding protein
c2: Iron stress-induced chlorophyll-binding protein
c3: Iron stress-induced chlorophyll-binding protein
c4: Iron stress-induced chlorophyll-binding protein
c5: Iron stress-induced chlorophyll-binding protein
c6: Iron stress-induced chlorophyll-binding protein
S: Iron stress-induced chlorophyll-binding protein
T: Iron stress-induced chlorophyll-binding protein
U: Iron stress-induced chlorophyll-binding protein
V: Iron stress-induced chlorophyll-binding protein
W: Iron stress-induced chlorophyll-binding protein
X: Iron stress-induced chlorophyll-binding protein
Y: Iron stress-induced chlorophyll-binding protein
Z: Iron stress-induced chlorophyll-binding protein
a: Iron stress-induced chlorophyll-binding protein
b: Iron stress-induced chlorophyll-binding protein
c: Iron stress-induced chlorophyll-binding protein
d: Iron stress-induced chlorophyll-binding protein
e: Iron stress-induced chlorophyll-binding protein
f: Iron stress-induced chlorophyll-binding protein
g: Iron stress-induced chlorophyll-binding protein
h: Iron stress-induced chlorophyll-binding protein
i: Iron stress-induced chlorophyll-binding protein
j: Iron stress-induced chlorophyll-binding protein
k: Iron stress-induced chlorophyll-binding protein
l: Iron stress-induced chlorophyll-binding protein
m: Iron stress-induced chlorophyll-binding protein
n: Iron stress-induced chlorophyll-binding protein
o: Iron stress-induced chlorophyll-binding protein
p: Iron stress-induced chlorophyll-binding protein
q: Iron stress-induced chlorophyll-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,566,2781433
Polymers2,464,33779
Non-polymers1,101,9411354
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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Photosystem I ... , 12 types, 36 molecules aAbAcAaBbBcBaCbCcCaDbDcDaEbEcEaFbFcFaIbIcIaJbJcJaKbKcKaLbLcL...

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


Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17716.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4297.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4770.698 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16261.685 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein


Mass: 4424.317 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DKP6

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Protein / Sugars , 2 types, 55 molecules a1a2a3a4a5a6b1b2b3b4b5b6c1c2c3c4c5c6STUVWXYZabcd...

#13: Protein ...
Iron stress-induced chlorophyll-binding protein / CP43'


Mass: 39284.332 Da / Num. of mol.: 43 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DK20
#19: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 1342 molecules

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


Mass: 893.489 Da / Num. of mol.: 1016 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 238 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#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.: 40 / Source method: obtained synthetically / Formula: C41H78O12S
#21: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#22: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: Complex of trimeric Photosystem I core associated with 43 iron stress-induced protein A
Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Buffer solutionpH: 7.5
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95950 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 58.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0017248932
ELECTRON MICROSCOPYf_angle_d0.4912354983
ELECTRON MICROSCOPYf_chiral_restr0.034230797
ELECTRON MICROSCOPYf_plane_restr0.003347651
ELECTRON MICROSCOPYf_dihedral_angle_d15.039573241

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