[English] 日本語
Yorodumi
- PDB-9xk9: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xk9
TitleIn situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
Components
  • (Chlorophyll a-b binding protein, ...) x 2
  • Chlorophyll a-b binding protein 2, chloroplastic
  • Chlorophyll a/b-binding protein
KeywordsPHOTOSYNTHESIS / Photosystem II / C2S2M2L4-type / M-LHCII / in situ / Oryza sativa / chloroplast
Function / homology
Function and homology information


photosynthesis, light harvesting / chloroplast thylakoid membrane / photosynthesis / mRNA binding
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-LUT / Chem-XAT / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 2, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsLi, J. / Elias, E. / Zhang, K. / Croce, R. / Zhu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201038 China
CitationJournal: Nature / Year: 2026
Title: In situ structures of plant photosystem supercomplexes.
Authors: Jiao Li / Eduard Elias / Kai Zhang / Roberta Croce / Jiapeng Zhu /
Abstract: Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although ...Photosynthesis sustains life on Earth by converting light to chemical energy through the coordinated action of photosystem I (PSI) and photosystem II (PSII) within thylakoid membranes. Although structures of isolated photosystems are available, their native organization in chloroplasts remains unknown. Here, using in situ cryo-electron microscopy, we directly imaged Oryza sativa (rice) chloroplasts and determined structures of photosystem supercomplexes in their native membrane environment. We resolved a CSML-type PSII-light harvesting complex II (LHCII) supercomplex, including four LHCII antenna trimers that were not retained in purified preparations. Excitation energy transfer calculations based on this architecture closely reproduce in vivo measurements, indicating its physiological relevance. We also resolved asymmetric PSII-LHCII dimers, including side-by-side, trans-lumenal and trans-stromal architectures, and higher-order assemblies of trimers and tetramers. On the basis of these observations, we propose that PSII forms a trans-lumenal and trans-stromal 'skeleton' that shapes thylakoid morphology and supports grana stacking. In addition, we obtained high-resolution structures of PSI-LHCI-LHCII and PSI-LHCI supercomplexes. Together, these structures reveal extensive networks of lipids, pigments and cofactors, providing the first molecular framework for understanding how the native architecture of plant photosystem supports the exceptional photon-to-electron efficiency of photosynthesis.
History
DepositionNov 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
05: Chlorophyll a-b binding protein 2, chloroplastic
06: Chlorophyll a-b binding protein 2, chloroplastic
07: Chlorophyll a/b-binding protein
08: Chlorophyll a-b binding protein, chloroplastic
1r: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,93673
Polymers119,4375
Non-polymers59,49968
Water00
1


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

-
Components

-
Protein , 2 types, 3 molecules 050607

#1: Protein Chlorophyll a-b binding protein 2, chloroplastic / LHCII type I CAB-2 / LHCP


Mass: 23441.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: P12331
#2: Protein Chlorophyll a/b-binding protein / cDNA clone:001-013-D02 / full insert sequence / cDNA clone:001-019-D10 / cDNA clone:001-203-F03 / ...cDNA clone:001-013-D02 / full insert sequence / cDNA clone:001-019-D10 / cDNA clone:001-203-F03 / cDNA clone:001-206-G05 / cDNA clone:006-301-C07 / cDNA clone:006-302-C03 / cDNA clone:006-306-E11 / cDNA clone:006-309-G12


Mass: 24065.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: B7E6H8

-
Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 081r

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


Mass: 22550.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q7XV11
#4: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25938.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Oryza sativa Japonica Group (Japanese rice)
References: UniProt: Q6Z411

-
Non-polymers , 5 types, 68 molecules

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


Mass: 893.489 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#9: Chemical ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O4 / 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: In situ C2S2M2L4-type PSII-LHCII supercomplex, moderately bound (M-) LHCII trimer with CP29 and CP24, protomer 2
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Buffer solutionpH: 7.3
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 1.375 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172752 / Symmetry type: POINT
RefinementHighest resolution: 3.64 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0199292
ELECTRON MICROSCOPYf_angle_d5.655139366
ELECTRON MICROSCOPYf_dihedral_angle_d15.77223729
ELECTRON MICROSCOPYf_chiral_restr0.22112953
ELECTRON MICROSCOPYf_plane_restr0.01416595

+
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