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- PDB-8vu3: Cryo-EM structure of cyanobacterial PSI with bound platinum nanop... -

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Basic information

Entry
Database: PDB / ID: 8vu3
TitleCryo-EM structure of cyanobacterial PSI with bound platinum nanoparticles
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Phosphorylase
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / cyanobacteria / biohybrid / platinum nanoparticles / hydrogen production / photosystem I / solar fuel
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase 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 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 PsaJ, reaction centre subunit IX superfamily / 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 PsaB / Photosystem I PsaA / 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 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit PsaK ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Phosphorylase / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesThermostichus lividus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsGisriel, C.J. / Malavath, T. / Brudvig, G.W. / Utschig, L.M.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE- AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140174 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst.
Authors: Christopher J Gisriel / Tirupathi Malavath / Tianyin Qiu / Jan Paul Menzel / Victor S Batista / Gary W Brudvig / Lisa M Utschig /
Abstract: Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex ...Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.
History
DepositionJan 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
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
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
N: Photosystem I iron-sulfur center
O: Photosystem I reaction center subunit II
P: Photosystem I reaction center subunit IV
Q: Photosystem I reaction center subunit III
R: Photosystem I reaction center subunit VIII
S: Photosystem I reaction center subunit IX
T: Photosystem I reaction center subunit PsaK
U: Photosystem I reaction center subunit XI
V: Photosystem I reaction center subunit XII
W: Phosphorylase
X: Phosphorylase
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
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
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
x: Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,914417
Polymers774,46736
Non-polymers305,447381
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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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules AGaBHb

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


Mass: 83195.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q201, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83152.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q1Z9, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 24 molecules DOdEPeFQfIRiJSjKTkLUlMVm

#4: Protein Photosystem I reaction center subunit II


Mass: 15408.582 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q2Y6
#5: Protein Photosystem I reaction center subunit IV


Mass: 8238.266 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q1I4
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17654.516 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2PYV7
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4480.442 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q0W5
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4965.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2PZG9
#9: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 8471.931 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q0K8
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16233.698 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q0R7
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3410.116 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A3B7MIX8

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Protein / Protein/peptide , 2 types, 6 molecules CNcWXx

#12: Protein/peptide Phosphorylase


Mass: 4134.966 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q2C6
#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) Thermostichus lividus (bacteria) / References: UniProt: A0A2D2Q1F9, photosystem I

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Non-polymers , 8 types, 381 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 285 / 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 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#20: 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 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: Photosystem I from Thermostichus lividus / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Thermostichus lividus (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189655 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00975738
ELECTRON MICROSCOPYf_angle_d1.997107610
ELECTRON MICROSCOPYf_dihedral_angle_d30.55718051
ELECTRON MICROSCOPYf_chiral_restr0.0769507
ELECTRON MICROSCOPYf_plane_restr0.01312951

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