[English] 日本語
Yorodumi
- PDB-6tcl: Photosystem I tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tcl
TitlePhotosystem I tetramer
Components(Photosystem I ...) x 18
KeywordsPHOTOSYNTHESIS / tetramer / anabaena / PSI
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 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / 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 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 4Fe-4S dicluster domain / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / 4Fe-4S dicluster domain / 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 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 PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / 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 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center / 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen, M. / Perez-Boerema, A. / Li, S. / Amunts, A.
Funding support Sweden, China, 5items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
National Natural Science Foundation of China (NSFC)21506113 China
National Natural Science Foundation of China (NSFC)31470229 China
CitationJournal: Nat Plants / Year: 2020
Title: Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.
Authors: Ming Chen / Annemarie Perez-Boerema / Laixing Zhang / Yanxue Li / Maojun Yang / Shizhong Li / Alexey Amunts /
Abstract: Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from ...Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 2.0May 22, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Non-polymer description / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10461
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: Photosystem I P700 chlorophyll a apoprotein A1
B1: Photosystem I P700 chlorophyll a apoprotein A2 1
C1: Photosystem I iron-sulfur center
D1: Photosystem I reaction center subunit II
E1: Photosystem I reaction center subunit IV
F1: Photosystem I reaction center subunit III
I1: Photosystem I reaction center subunit VIII
J1: Photosystem I reaction center subunit IX
K1: Photosystem I reaction center subunit PsaK 1
L1: Photosystem I reaction center subunit XI
M1: Photosystem I reaction center subunit XII
X1: Photosystem I 4.8 kDa protein
A2: Photosystem I P700 chlorophyll a apoprotein A1
B2: Photosystem I P700 chlorophyll a apoprotein A2 1
C2: Photosystem I iron-sulfur center
D2: Photosystem I reaction center subunit II
E2: Photosystem I reaction center subunit IV
F2: Photosystem I reaction center subunit III
I2: Photosystem I reaction center subunit VIII
J2: Photosystem I reaction center subunit IX
K2: Photosystem I reaction center subunit PsaK 1
L2: Photosystem I reaction center subunit XI
M2: Photosystem I reaction center subunit XII
X2: Photosystem I 4.8 kDa protein
A: Photosystem I P700 chlorophyll a apoprotein A1
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
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 1
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I 4.8 kDa protein
AA: Photosystem I P700 chlorophyll a apoprotein A1
BB: Photosystem I P700 chlorophyll a apoprotein A2 1
CC: Photosystem I iron-sulfur center
DD: Photosystem I reaction center subunit II
EE: Photosystem I reaction center subunit IV
FF: Photosystem I reaction center subunit III
II: Photosystem I reaction center subunit VIII
JJ: Photosystem I reaction center subunit IX
KK: Photosystem I reaction center subunit PsaK 1
LL: Photosystem I reaction center subunit XI
MM: Photosystem I reaction center subunit XII
XX: Photosystem I 4.8 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,478,636626
Polymers1,006,91948
Non-polymers471,717578
Water00
1


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

-
Components

-
Photosystem I ... , 18 types, 48 molecules A1A2AAAB1B2BBBC1C2CCCD1D2DDDE1E2F1FFFI1IIIJ1J2JJJK1K...

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


Mass: 81932.125 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58576, photosystem I
#2: Protein
Photosystem I P700 chlorophyll a apoprotein A2 1 / PsaB 1


Mass: 83254.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58565, photosystem I
#3: Protein
Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8694.010 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P0A410, photosystem I
#4: Protein
Photosystem I reaction center subunit II


Mass: 14672.670 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58573
#5: Protein Photosystem I reaction center subunit IV


Mass: 6809.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58575
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 15030.004 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58564
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3550.169 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58560
#8: Protein/peptide
Photosystem I reaction center subunit IX


Mass: 5368.227 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58568
#9: Protein Photosystem I reaction center subunit PsaK 1 / Photosystem I subunit X 1


Mass: 7580.861 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58583
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 17545.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58577
#11: Protein/peptide
Photosystem I reaction center subunit XII / PSI-M


Mass: 3407.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: Q8YNB0
#12: Protein/peptide
Photosystem I 4.8 kDa protein


Mass: 4342.132 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58566
#13: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 14845.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58564
#14: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3764.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58560
#15: Protein Photosystem I reaction center subunit PsaK 1 / Photosystem I subunit X 1


Mass: 7509.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58583
#16: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 17673.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58577
#17: Protein Photosystem I reaction center subunit IV


Mass: 7106.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58575
#18: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16290.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / References: UniProt: P58577

-
Sugars , 1 types, 2 molecules

#28: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 9 types, 576 molecules

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


Mass: 893.489 Da / Num. of mol.: 378 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#20: Chemical
ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#21: 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
#22: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: C40H56
#24: Chemical...
ChemComp-AJP / Digitonin


Mass: 1229.312 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#25: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H54O
#27: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Photosystem I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
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
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameCategory
2EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 428587
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69247 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004204779
ELECTRON MICROSCOPYf_angle_d1.2298373519
ELECTRON MICROSCOPYf_chiral_restr0.251413142
ELECTRON MICROSCOPYf_plane_restr0.004127325
ELECTRON MICROSCOPYf_dihedral_angle_d18.882971574

+
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