[English] 日本語
Yorodumi
- PDB-7f4v: Cryo-EM structure of a primordial cyanobacterial photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f4v
TitleCryo-EM structure of a primordial cyanobacterial photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • Photosystem I iron-sulfur center
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily ...Outer membrane protein, bacterial / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 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 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 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
Menaquinone-4 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit Z / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 ...Menaquinone-4 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit Z / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsKato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Yonekura, K. / Shen, J.R.
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI
Authors: Kato, K. / Hamaguchi, T. / Nagao, R. / Kawakami, K. / Ueno, Y. / Suzuki, T. / Uchida, H. / Murakami, A. / Nakajima, Y. / Yokono, M. / Akimoto, S. / Dohmae, N. / Yonekura, K. / Shen, J.R.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 Z
aJ: Unknown protein
aL: Photosystem I reaction center subunit XI
aM: Photosystem I reaction center subunit XII
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 Z
bJ: Unknown protein
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
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 Z
cJ: Unknown protein
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,067,066384
Polymers781,59130
Non-polymers285,475354
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB

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


Mass: 86505.219 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT6, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 96166.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFT5, photosystem I

-
Photosystem I reaction center subunit ... , 6 types, 18 molecules aDbDcDaEbEcEaFbFcFaIbIcIaLbLcLaMbMcM

#4: Protein Photosystem I reaction center subunit II


Mass: 15952.242 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NF26
#5: Protein Photosystem I reaction center subunit IV


Mass: 7468.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NFW6
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 19931.127 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NH05
#7: Protein/peptide Photosystem I reaction center subunit Z / PSI-Z


Mass: 3853.611 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: P0C029
#9: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15806.324 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NIE7
#10: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3212.907 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NHY3

-
Protein / Protein/peptide , 2 types, 6 molecules aCbCcCaJbJcJ

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8807.170 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / References: UniProt: Q7NG86, photosystem I
#8: Protein/peptide Unknown protein


Mass: 2826.475 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421

-
Non-polymers , 8 types, 756 molecules

#11: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


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


Mass: 893.489 Da / Num. of mol.: 264 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical
ChemComp-1L3 / Menaquinone-4 / vitamin K2


Mass: 444.648 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H40O2
#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PSI trimer / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.03 %DDM1
SpecimenConc.: 1.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 70.22 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.13_2998model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261743 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
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