[English] 日本語
Yorodumi
- PDB-9s3e: Universal Photosystem II Intermediate with Light-Dependent Water-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s3e
TitleUniversal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Pisum sativum
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 12
  • PSII 6.1 kDa protein
  • Ultraviolet-B-repressible protein
KeywordsPHOTOSYNTHESIS / Higher plants / PSII / Pisum sativum / membrane protein / Cryo-EM / assembly intermediate / water-ferrocyanide oxido-reductase.
Function / homology
Function and homology information


photoinhibition / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide ...photoinhibition / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / poly(U) RNA binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily ...Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II reaction center protein I / Photosystem II 5 kDa protein, chloroplastic / PSII 6.1 kDa protein / Ultraviolet-B-repressible protein / Photosystem II reaction center protein K / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / 16 kDa subunit of oxygen evolving system of photosystem II / Photosystem II reaction center protein T / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsNelson, N. / Klaiman, D. / Fadeeva, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Pisum sativum
Authors: Nelson, N. / Klaiman, D. / Fadeeva, M.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1, chloroplastic
P: Oxygen-evolving enhancer protein 2, chloroplastic
Q: Oxygen-evolving enhancer protein 3
T: Photosystem II reaction center protein T
W: PSII 6.1 kDa protein
X: Ultraviolet-B-repressible protein
U: Photosystem II 5 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,87889
Polymers293,27319
Non-polymers53,60570
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Photosystem II ... , 12 types, 12 molecules ABCDHIJKLMTU

#1: Protein Photosystem II protein D1 / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 36972.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06585, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 53157.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL6
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Photosystem II 44 kDa chlorophyll apoprotein / Protein CP-43


Mass: 49174.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06004
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38106.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P06006, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein / Photosystem II 9 kDa phosphoprotein


Mass: 6455.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9XQR3
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3769.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A2S1CE74
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3598.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13555
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4287.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAJ8
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4137.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P60147
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3066.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P69529
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3462.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q8HS25
#19: Protein/peptide Photosystem II 5 kDa protein, chloroplastic


Mass: 3080.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A9D4VSA9

-
Cytochrome b559 subunit ... , 2 types, 2 molecules EF

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 8624.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P13554
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3396.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P62096

-
Oxygen-evolving enhancer protein ... , 3 types, 3 molecules OPQ

#13: Protein Oxygen-evolving enhancer protein 1, chloroplastic / OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane ...OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / OEC 33 kDa subunit


Mass: 26554.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P14226
#14: Protein Oxygen-evolving enhancer protein 2, chloroplastic / OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane ...OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane protein / OEC 23 kDa subunit


Mass: 20287.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P16059
#15: Protein Oxygen-evolving enhancer protein 3


Mass: 16398.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q7Y1T5

-
Protein/peptide , 2 types, 2 molecules WX

#17: Protein/peptide PSII 6.1 kDa protein


Mass: 5198.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A9D4W3H0
#18: Protein/peptide Ultraviolet-B-repressible protein


Mass: 3544.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A9D4X981

-
Sugars , 1 types, 4 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 13 types, 844 molecules

#20: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CaMn4O5
#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#22: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#24: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#25: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56
#26: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#27: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#28: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#29: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10
#30: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#32: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: Photosystem II Intermediate / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 0.35 MDa / Experimental value: YES
Source (natural)Organism: Pisum sativum (garden pea)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Chlorophyll concentration
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 288 K

-
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 magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 24215

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.21.2_5419model refinement
5CTFFIND4CTF correction
10UCSF Chimerainitial Euler assignment
11PHENIXfinal Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7825226
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 323534 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 2.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00825293
ELECTRON MICROSCOPYf_angle_d1.5634751
ELECTRON MICROSCOPYf_dihedral_angle_d22.2839677
ELECTRON MICROSCOPYf_chiral_restr0.083462
ELECTRON MICROSCOPYf_plane_restr0.0194217

+
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