[English] 日本語
Yorodumi
- PDB-7wzn: PSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wzn
TitlePSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 8
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 4
  • Ferredoxin, chloroplastic
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / membrane supercomplex / light harvesting / electron transport / green algae
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / iron-sulfur cluster binding / response to light stimulus / photosynthesis / chloroplast / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / Ferredoxin [2Fe-2S], plant / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily ...Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / Ferredoxin [2Fe-2S], plant / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / 4Fe-4S dicluster domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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
CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chlorophyll a-b binding protein, chloroplastic / Ferredoxin, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 ...CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chlorophyll a-b binding protein, chloroplastic / Ferredoxin, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsKurisu, G. / Gerle, C. / Mitsuoka, K. / Kawamoto, A. / Tanaka, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR13M4 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Nanotechnology Platform Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2023
Title: Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin.
Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun ...Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun Minagawa / Genji Kurisu /
Abstract: Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural ...Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.
History
DepositionFeb 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: pdbx_database_related
Revision 1.2Jul 5, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 12, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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, chloroplastic
E: Photosystem I reaction center subunit IV, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
J: Photosystem I reaction center subunit IX
1: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
Z: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
G: Ferredoxin, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)651,127227
Polymers465,60616
Non-polymers185,521211
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 83239.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12154, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82184.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09144, photosystem I

-
Protein , 2 types, 2 molecules CG

#3: Protein Photosystem I iron-sulfur center / / PsaC


Mass: 8869.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q00914, photosystem I
#16: Protein Ferredoxin, chloroplastic /


Mass: 13243.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PETF / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07839

-
Photosystem I reaction center subunit ... , 4 types, 4 molecules DEFJ

#4: Protein Photosystem I reaction center subunit II, chloroplastic / / Photosystem I 20 kDa subunit / PSI-D


Mass: 21372.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39615
#5: Protein Photosystem I reaction center subunit IV, chloroplastic / / PSI-E / P30 protein / Photosystem I 8.1 kDa protein


Mass: 10786.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12352
#6: Protein Photosystem I reaction center subunit III, chloroplastic / / Light-harvesting complex I 17 kDa protein / P21 protein / PSI-F


Mass: 24088.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12356
#7: Protein/peptide Photosystem I reaction center subunit IX / / Photosystem I reaction center subunit J / PSI-J


Mass: 4750.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59777

-
Chlorophyll a-b binding protein, ... , 8 types, 8 molecules 1378Z456

#8: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23520.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7DM26
#9: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 32629.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF10
#10: Protein Chlorophyll a-b binding protein, chloroplastic / Lhca7


Mass: 26248.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84Y02
#11: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25948.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY7
#12: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23923.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q05093
#13: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 28729.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VZ0
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 28257.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY8
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27812.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q75VY6

-
Non-polymers , 6 types, 211 molecules

#17: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 188 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.COMPLEXMembrane supercomplex purified without column use under green light conditions, stabilized by the mild detergent GDN with excess detergent removed using GraDeR and pre-plunge freezing added ferredoxin.#1-#160MULTIPLE SOURCES
2Membrane supercomplexCOMPLEX#1-#151NATURAL
3ferredoxinCOMPLEX#161RECOMBINANT
Molecular weightValue: 0.785 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellular locationOrganelle
12Chlamydomonas reinhardtii (plant)3055Wild Type strain 137cThylakoid membraneChloroplast
23Chlamydomonas reinhardtii (plant)3055Chloroplast
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMMESC6H13NO4S1
20.02 %GDNC56H92O251
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was monodisperse with a low level of contaminants and excess free detergent removed using the GraDeR approach.
Specimen supportDetails: Glow discharge on both sides at 5 mA for 90 seconds each.
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: 2.6 microliter of sample were applied to cryo-grids and blotted for 3.5 seconds using Whatman #1 before plunge freezing.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Preliminary grid screening was performed manually using a JEOL JEM-3000SFF microscope.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 91 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2646
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11cryoSPARC2initial Euler assignment
12cryoSPARC2final Euler assignment
13cryoSPARC2classification
14cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 857909
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48941 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6JO5

6jo5

RefinementHighest resolution: 4.9 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more