[English] 日本語
Yorodumi
- PDB-8xls: PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xls
TitlePSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335
Components
  • (Fucoxanthin chl a/c light-harvesting ...) x 2
  • (Fucoxanthin chlorophyll a/c-binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
  • Pt17531-like protein
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus ...light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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
: / Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...: / Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Fucoxanthin chl a/c light-harvesting protein, major type / Uncharacterized protein / Fucoxanthin chl a/c light-harvesting protein / Uncharacterized protein / Pt17531-like protein
Similarity search - Component
Biological speciesThalassiosira pseudonana CCMP1335 (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKato, K. / Nakajima, Y. / Shen, J.R. / Nagao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2024
Title: Structural basis for molecular assembly of fucoxanthin chlorophyll /-binding proteins in a diatom photosystem I supercomplex.
Authors: Koji Kato / Yoshiki Nakajima / Jian Xing / Minoru Kumazawa / Haruya Ogawa / Jian-Ren Shen / Kentaro Ifuku / Ryo Nagao /
Abstract: Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI ...Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll /-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from and the diatom , underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.
History
DepositionDec 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / em_admin / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_stereo_config / _chem_comp_bond.value_order / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.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
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
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
W: Photosystem I reaction center subunit Psa29
u: Unknown protein
1: Fucoxanthin chlorophyll a/c-binding protein RedCAP
2: Fucoxanthin chl a/c light-harvesting protein
3: Pt17531-like protein
4: Fucoxanthin chl a/c light-harvesting protein, major type
5: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,618313
Polymers382,08117
Non-polymers164,537296
Water16,610922
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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: 83725.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0M8, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82173.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0M9, photosystem I

-
Protein , 3 types, 3 molecules Cu3

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


Mass: 8807.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0W4, photosystem I
#12: Protein Unknown protein


Mass: 7166.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
#15: Protein Pt17531-like protein / Fucoxanthin chlorophyll a/c-binding protein Lhcq10


Mass: 21210.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8CEQ3

-
Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLMW

#4: Protein Photosystem I reaction center subunit II


Mass: 15535.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0T5
#5: Protein Photosystem I reaction center subunit IV


Mass: 7520.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0P9
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20382.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0V0
#7: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3919.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0S9
#8: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4854.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0V1
#9: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15715.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0U5
#10: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3271.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: A0T0S1
#11: Protein Photosystem I reaction center subunit Psa29


Mass: 20048.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8BUW3

-
Fucoxanthin chlorophyll a/c-binding protein ... , 2 types, 2 molecules 15

#13: Protein Fucoxanthin chlorophyll a/c-binding protein RedCAP


Mass: 23695.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
#17: Protein Fucoxanthin chlorophyll a/c-binding protein Lhcq8


Mass: 21112.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C770

-
Fucoxanthin chl a/c light-harvesting ... , 2 types, 2 molecules 24

#14: Protein Fucoxanthin chl a/c light-harvesting protein


Mass: 21438.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B8C2K6
#16: Protein Fucoxanthin chl a/c light-harvesting protein, major type


Mass: 21502.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thalassiosira pseudonana CCMP1335 (Diatom)
References: UniProt: B5YM25

-
Sugars , 2 types, 5 molecules

#24: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#26: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 13 types, 1213 molecules

#18: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 138 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#20: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#22: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#25: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 89 / Source method: obtained synthetically
#27: Chemical ChemComp-5X6 / Zeaxanthin / (1R)-4-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4R)-4-hydroxy-2,6,6-trimethylcyclohexen-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#28: Chemical
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H54O3
#29: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#30: Chemical
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#31: Chemical
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C42H58O6
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 922 / 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-FCPI / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: NO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESMES-NaOH1
20.03 %DDMDDM1
SpecimenConc.: 3 mg/ml / Embedding 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
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 / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.16model fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13Servalcat0.4.32model refinement
14REFMAC5.8.0419model refinement
15PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2733572
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75667 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: experimental model

+
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