[English] 日本語
Yorodumi
- PDB-9i4t: Photosystem II from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i4t
TitlePhotosystem II from Arabidopsis thaliana
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 14
  • Expressed protein
KeywordsPHOTOSYNTHESIS / Membrane bound / Photosystem II / Arabidopsis / Manganese cluster / oxidoreductase
Function / homology
Function and homology information


response to desiccation / photosystem I assembly / chloroplast photosystem II / photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / response to red light / cellular response to abscisic acid stimulus / cellular response to water deprivation / nonphotochemical quenching ...response to desiccation / photosystem I assembly / chloroplast photosystem II / photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / response to red light / cellular response to abscisic acid stimulus / cellular response to water deprivation / nonphotochemical quenching / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / response to low light intensity stimulus / thylakoid lumen / plastid thylakoid membrane / salicylic acid binding / plastoglobule / regulation of stomatal closure / response to far red light / thylakoid membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II assembly / apoplast / chloroplast thylakoid lumen / thylakoid / oxygen evolving activity / photosystem II stabilization / protein phosphatase regulator activity / photosystem II reaction center / photosystem II / chloroplast envelope / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / response to herbicide / photosystem II / extrinsic component of membrane / poly(U) RNA binding / chloroplast stroma / plastid / photosynthetic electron transport in photosystem II / positive regulation of reactive oxygen species biosynthetic process / chlorophyll binding / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / calcium ion binding / mitochondrion / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
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 PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding 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 B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein J / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Oxygen-evolving enhancer protein 2-1, chloroplastic / Chlorophyll a-b binding protein 2.1, chloroplastic / Expressed protein / Chlorophyll a-b binding protein CP26, chloroplastic / Oxygen-evolving enhancer protein 3-1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsForsman, J.A. / Graca, A.T. / Hussein, R. / Hall, M. / Messinger, J. / Schroder, W.P. / Aydin, A.O.
Funding support Sweden, Germany, 5items
OrganizationGrant numberCountry
Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden
Swedish Research Council2020-03809 Sweden
Carl Trygger FoundationCTS 19.324 Sweden
Kempe FoundationJCK-2030 Sweden
German Research Foundation (DFG)TP A5 Germany
CitationJournal: New Phytol / Year: 2026
Title: The structure of intact and active Photosystem II from Arabidopsis thaliana at 2.44 Å resolution.
Authors: Jack Forsman / André T Graça / Abuzer Orkun Aydin / Michael Hall / Rana Hussein / Wolfgang P Schröder / Johannes Messinger /
Abstract: Photosystem II (PS II) is a large membrane-bound protein complex that catalyses light-driven water oxidation in plants and cyanobacteria. The structure of PS II is well studied in cyanobacteria; ...Photosystem II (PS II) is a large membrane-bound protein complex that catalyses light-driven water oxidation in plants and cyanobacteria. The structure of PS II is well studied in cyanobacteria; however, there are very few PS II structures from plants. The currently available plant PS II structures are comparatively low resolution and are frequently incomplete, that is, missing subunits or cofactors. We optimized the procedure for isolating PS II from Arabidopsis thaliana and employed cryo-electron microscopy to generate a high-resolution structure of an intact and oxygen-evolving PS II from Arabidopsis thaliana at 2.44 Å resolution, which to date represents the highest resolution structure of PS II from higher plants. At this resolution, many water molecules within the PS II structure can be detected, including waters around the water-splitting manganese cluster, the nonheme iron, and within the water/proton channels connecting these active sites to the protein exterior, allowing for the first detailed description of the water networks in Arabidopsis thaliana and comparison with the highly resolved cyanobacterial PS II. Our findings further the understanding of design principles of protein-water-cofactor interactions in photosynthetic water splitting, quinone reduction/exchange, and about the role of lipids at the interface between PS II and the light-harvesting proteins.
History
DepositionJan 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Data collection / Database references
Category: chem_comp_atom / citation ...chem_comp_atom / citation / citation_author / em_admin / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_stereo_config / _citation.country ..._chem_comp_atom.pdbx_stereo_config / _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 / _citation_author.name / _em_admin.last_update
Revision 1.1Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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 / _citation_author.name / _em_admin.last_update

-
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
G: Chlorophyll a-b binding protein 1, chloroplastic
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
N: Chlorophyll a-b binding protein 1, chloroplastic
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
P: Oxygen-evolving enhancer protein 2-1, chloroplastic
Q: Oxygen-evolving enhancer protein 3-1, chloroplastic
R: Chlorophyll a-b binding protein CP29.1, chloroplastic
S: Chlorophyll a-b binding protein CP26, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
W: Photosystem II reaction center W protein, chloroplastic
X: Expressed protein
Y: Chlorophyll a-b binding protein 2.1, chloroplastic
Z: Photosystem II reaction center protein Z
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
g: Chlorophyll a-b binding protein 1, chloroplastic
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
n: Chlorophyll a-b binding protein 1, chloroplastic
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
p: Oxygen-evolving enhancer protein 2-1, chloroplastic
q: Oxygen-evolving enhancer protein 3-1, chloroplastic
r: Chlorophyll a-b binding protein CP29.1, chloroplastic
s: Chlorophyll a-b binding protein CP26, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
w: Photosystem II reaction center W protein, chloroplastic
x: Expressed protein
y: Chlorophyll a-b binding protein 2.1, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,288,897382
Polymers1,024,74350
Non-polymers264,154332
Water21,7261206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Photosystem II ... , 14 types, 28 molecules AaBbCcDdHhIiJjKkLlMmTtUuWwZz

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38961.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P83755, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56777
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 51915.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56778
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39575.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56761, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7706.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56780
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62100
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4117.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56781
#11: Protein Photosystem II reaction center protein K / PSII-K


Mass: 6977.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56782
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P60129
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62109
#19: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P61839
#20: Protein Photosystem II 5 kDa protein, chloroplastic / PSII-T / Nuclear encoded psbT / PsbTn


Mass: 11042.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q39195
#21: Protein Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 13685.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q39194
#24: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56790

-
Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

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


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56779
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4488.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62095

-
Chlorophyll a-b binding protein ... , 4 types, 10 molecules GNgnRrSsYy

#7: Protein
Chlorophyll a-b binding protein 1, chloroplastic / Chlorophyll a-b protein 140 / CAB-140 / LHCII type I CAB-1


Mass: 28266.062 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P04778
#17: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 31170.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q07473
#18: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 30187.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9XF89
#23: Protein Chlorophyll a-b binding protein 2.1, chloroplastic / Photosystem II light harvesting complex gene 2.1 / Protein LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2.1


Mass: 28673.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9SHR7

-
Oxygen-evolving enhancer protein ... , 3 types, 6 molecules OoPpQq

#14: Protein Oxygen-evolving enhancer protein 1-1, 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 / Manganese-stabilizing protein 1 / MSP-1 / OEC 33 kDa subunit


Mass: 35180.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P23321
#15: Protein Oxygen-evolving enhancer protein 2-1, 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 / OEC23


Mass: 28125.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q42029
#16: Protein Oxygen-evolving enhancer protein 3-1, chloroplastic / OEE3 / 16 kDa subunit of oxygen evolving system of photosystem II / OEC 16 kDa subunit


Mass: 23899.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9XFT3

-
Protein , 1 types, 2 molecules Xx

#22: Protein Expressed protein / PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein ...PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein At2g06520 / T12H3.7


Mass: 11826.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9SKI3

-
Sugars , 2 types, 12 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#36: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 17 types, 1526 molecules

#25: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#26: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#28: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#29: 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#30: 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.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#31: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: 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.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#41: 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.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#42: Chemical
ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#43: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / Source method: isolated from a natural source / Formula: H2O

-
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: C2S2-type Photosystem II complex from Arabidopsis thaliana
Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 1.118 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Organelle: Thylakoid membranes / Tissue: Leaves
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-(N-morpholino)ethanesulfonic acidC6H13NO4S1
220 mMCalcium ChlorideCaCl21
35 mMMagnesium ChlorideMgCl21
40.6 MBetaineC5H11NO21
50.03 % w/vn-Dodecyl-b-D-maltosideC24H46O111
SpecimenConc.: 9.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Thylakoid membranes were solubilised using b-dodecylmaltoside. The C2S2-type Photosystem II complexes were isolated using sucrose gradients.
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 200 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

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: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.17 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16450
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCparticle selection
2EPU3.4image acquisitionAFIS
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3054062
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72301 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3JCU

3jcu


Accession code: 3JCU / Source name: PDB / 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