[English] 日本語
Yorodumi
- PDB-8jjr: Cryo-EM structure of Symbiodinium photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jjr
TitleCryo-EM structure of Symbiodinium photosystem I
Components
  • PCP-11
  • PCPI-1
  • PCPI-10
  • PCPI-12
  • PCPI-13
  • PCPI-2
  • PCPI-3
  • PCPI-4
  • PCPI-5
  • PCPI-6
  • PCPI-7
  • PCPI-8
  • PCPI-9
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaI
  • PsaJ
  • PsaL
  • PsaM
  • PsaR
  • PsaT
  • PsaU
KeywordsPHOTOSYNTHESIS / Symbiodinium / Photosystem I
Function / homology
Function and homology information


BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / :
Similarity search - Component
Biological speciesSymbiodinium sp. (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhao, L.S. / Wang, N. / Li, K. / Zhang, Y.Z. / Liu, L.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2024
Title: Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.
Authors: Long-Sheng Zhao / Ning Wang / Kang Li / Chun-Yang Li / Jian-Ping Guo / Fei-Yu He / Gui-Ming Liu / Xiu-Lan Chen / Jun Gao / Lu-Ning Liu / Yu-Zhong Zhang /
Abstract: Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral ...Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PCPI-7
B: PCPI-1
C: PCP-11
D: PCPI-6
E: PCPI-5
F: PCPI-8
G: PCPI-4
H: PCPI-10
I: PCPI-3
J: PCPI-9
K: PCPI-13
T: PCPI-12
U: PCPI-2
a: PsaA
b: PsaB
c: PsaC
d: PsaD
e: PsaE
f: PsaF
i: PsaI
j: PsaJ
l: PsaL
m: PsaM
r: PsaR
x: PsaT
y: PsaU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)958,334349
Polymers704,34026
Non-polymers253,994323
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 26 types, 26 molecules ABCDEFGHIJKTUabcdefijlmrxy

#1: Protein PCPI-7


Mass: 27129.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#2: Protein PCPI-1


Mass: 28182.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#3: Protein PCP-11


Mass: 21707.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#4: Protein PCPI-6


Mass: 19572.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#5: Protein PCPI-5


Mass: 26752.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#6: Protein PCPI-8


Mass: 30544.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#7: Protein PCPI-4


Mass: 24445.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#8: Protein PCPI-10


Mass: 27998.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#9: Protein PCPI-3


Mass: 27409.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#10: Protein PCPI-9


Mass: 22091.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#11: Protein PCPI-13


Mass: 23286.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#12: Protein PCPI-12


Mass: 21881.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#13: Protein PCPI-2


Mass: 15403.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#14: Protein PsaA


Mass: 76579.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#15: Protein PsaB


Mass: 74857.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#16: Protein PsaC


Mass: 16733.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#17: Protein PsaD


Mass: 32748.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#18: Protein PsaE


Mass: 13089.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#19: Protein PsaF


Mass: 29733.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#20: Protein PsaI


Mass: 19725.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#21: Protein PsaJ


Mass: 15832.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#22: Protein PsaL


Mass: 38708.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#23: Protein PsaM


Mass: 14969.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#24: Protein PsaR


Mass: 17253.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#25: Protein PsaT


Mass: 13400.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)
#26: Protein PsaU


Mass: 24303.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium sp. (eukaryote)

-
Sugars , 2 types, 5 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15
#36: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 11 types, 318 molecules

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


Mass: 893.489 Da / Num. of mol.: 196 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-UIX / [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate / Dinoxanthin


Mass: 642.907 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H58O5 / Feature type: SUBJECT OF INVESTIGATION
#30: 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.: 41 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78O12S
#32: Chemical
ChemComp-PID / PERIDININ


Mass: 630.810 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C39H50O7 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#34: 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
#37: 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 / Feature type: SUBJECT OF INVESTIGATION
#38: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Photosystem I of Symbiodinium / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Symbiodinium sp. (eukaryote)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161863 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00858982
ELECTRON MICROSCOPYf_angle_d1.09883744
ELECTRON MICROSCOPYf_dihedral_angle_d12.80818942
ELECTRON MICROSCOPYf_chiral_restr0.0817444
ELECTRON MICROSCOPYf_plane_restr0.00617877

+
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