[English] 日本語
Yorodumi
- EMDB-81438: In situ structure of the side-by-side PSII-LHCII dimer from Oryza... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-81438
TitleIn situ structure of the side-by-side PSII-LHCII dimer from Oryza sativa (composite)
Map data
Sample
  • Complex: Chloroplast
    • Protein or peptide: x 10 types
  • Protein or peptide: x 16 types
  • Ligand: x 1 types
KeywordsPhotosystem II / in situ / side-by-side / Oryza sativa / Chloroplast / Photosynthesis
Function / homology
Function and homology information


chloroplast photosystem II / chloroplast thylakoid / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain ...chloroplast photosystem II / chloroplast thylakoid / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / extrinsic component of membrane / chlorophyll binding / plastid / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / mRNA binding / heme binding / calcium ion binding
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / 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) / Photosystem II protein Y (PsbY) ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / 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) / Photosystem II protein Y (PsbY) / Photosystem II PsbY / 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 reaction centre protein H / Photosystem II protein D1 / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / Chlorophyll A-B binding protein, plant and chromista / : / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
cDNA clone:001-024-H10, full insert sequence / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II reaction center protein M / Photosystem II reaction center protein J ...cDNA clone:001-024-H10, full insert sequence / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II reaction center protein M / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein H / Photosystem II reaction center protein T / Photosystem II reaction center protein Z / Photosystem II protein D1 / Photosystem II D2 protein / Chlorophyll a-b binding protein 2, chloroplastic / Os02g0581100 protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Os07g0673550 protein / Chlorophyll a-b binding protein, chloroplastic / 23 kDa subunit of oxygen evolving system of photosystem II / Photosystem II 10 kDa polypeptide, chloroplastic / 33 kDa subunit of oxygen evolving system of photosystem II
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi J / Elias E / Zhang K / Croce R / Zhu J
Funding support China, 1 items
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
DepositionJun 12, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_81438.png

Downloads & links

-
Map

FileDownload / File: emd_81438.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 512 pix.
= 655.36 Å		1.28 Å/pix.
x 512 pix.
= 655.36 Å		1.28 Å/pix.
x 512 pix.
= 655.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0005
Minimum - Maximum-0.07392051 - 0.47752222
Average (Standard dev.)0.000948279 (±0.010140587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 655.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_81438_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_81438_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Chloroplast

EntireName: Chloroplast
Components
  • Complex: Chloroplast
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: 33 kDa subunit of oxygen evolving system of photosystem II
    • Protein or peptide: Os02g0581100 protein
    • Protein or peptide: Os07g0673550 protein
    • Protein or peptide: cDNA clone:001-024-H10, full insert sequence
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: 23 kDa subunit of oxygen evolving system of photosystem II
    • Protein or peptide: Photosystem II 10 kDa polypeptide, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein 2, chloroplastic
  • Protein or peptide: Chlorophyll a/b-binding protein
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Photosystem II protein D1
  • Protein or peptide: Photosystem II CP47 reaction center protein
  • Protein or peptide: Photosystem II CP43 reaction center protein
  • Protein or peptide: Photosystem II D2 protein
  • Protein or peptide: Cytochrome b559 subunit beta
  • Protein or peptide: Photosystem II reaction center protein H
  • Protein or peptide: Photosystem II reaction center protein I
  • Protein or peptide: Photosystem II reaction center protein J
  • Protein or peptide: Photosystem II reaction center protein L
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Photosystem II reaction center protein T
  • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
  • Ligand: BICARBONATE ION

+
Supramolecule #1: Chloroplast

SupramoleculeName: Chloroplast / type: complex / ID: 1 / Parent: 0
Macromolecule list: #8, #13, #15-#16, #21, #24-#26, #17, #22
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

+
Macromolecule #1: Chlorophyll a-b binding protein 2, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 23.441461 KDa
SequenceString: GSPWYGADRV LYLGPLSGEP PSYLTGEFPG DYGWDTAGLS ADPETFAKNR ELEVIHSRWA MLGALGCVFP ELLARNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLIHA QSILAIWAVQ VVLMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE ...String:
GSPWYGADRV LYLGPLSGEP PSYLTGEFPG DYGWDTAGLS ADPETFAKNR ELEVIHSRWA MLGALGCVFP ELLARNGVKF GEAVWFKAG SQIFSEGGLD YLGNPSLIHA QSILAIWAVQ VVLMGAVEGY RIAGGPLGEV VDPLYPGGSF DPLGLADDPE A FAELKVKE IKNGRLAMFS MFGFFVQAIV TGKGPLENLA DHLADPVNNN AWAYATNFVP G

UniProtKB: Chlorophyll a-b binding protein 2, chloroplastic

+
Macromolecule #2: Chlorophyll a/b-binding protein

MacromoleculeName: Chlorophyll a/b-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 24.065338 KDa
SequenceString: ELWYGPDRVK YLGPFSAQTP SYLRGEFPGD YGWDTAGLSA DPEAFARNRA LEVIHGRWAM LGALGCITPE VLEKWVRVDF KEPVWFKAG AQIFSDGGLD YLGNPNLVHA QSILAVLGFQ VVLMGLVEGY RINGLPGVGD GNDLYPGGQY FDPLGLADDP V TFAELKVK ...String:
ELWYGPDRVK YLGPFSAQTP SYLRGEFPGD YGWDTAGLSA DPEAFARNRA LEVIHGRWAM LGALGCITPE VLEKWVRVDF KEPVWFKAG AQIFSDGGLD YLGNPNLVHA QSILAVLGFQ VVLMGLVEGY RINGLPGVGD GNDLYPGGQY FDPLGLADDP V TFAELKVK EIKNGRLAMF SMFGFFVQAI VTGKGPLENL LDHLADPVAN NAWVYATKFT PG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 22.55058 KDa
SequenceString: AKKSWIPAFK SDAEFINPPW LDGSLPGDFG FDPLGLGKDP AFLKWYREAE LIHGRWAMAA VLGIFVGQAW SGVPWFEAGA QPEAIAPFS FGSLLGTQLL LMGWVESKRW VDFFNPDSQA VEWATPWSRT AENFSNATGE QGYPGGKFFD PLGLGGETRD G VYIPDTDK ...String:
AKKSWIPAFK SDAEFINPPW LDGSLPGDFG FDPLGLGKDP AFLKWYREAE LIHGRWAMAA VLGIFVGQAW SGVPWFEAGA QPEAIAPFS FGSLLGTQLL LMGWVESKRW VDFFNPDSQA VEWATPWSRT AENFSNATGE QGYPGGKFFD PLGLGGETRD G VYIPDTDK LDRLKLAEIK HARLAMLAML IFYFEAGQGK TPLGALG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #4: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 36.917039 KDa
SequenceString: TSLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL IYPIGQGSFS D GMPLGISG ...String:
TSLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL IYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGIWFTA LGISTMAFNL NGFNFNQSVV DSQGRVINTW ADIINRANLG MEV MHERNA HNFPLDLA

UniProtKB: Photosystem II protein D1

+
Macromolecule #5: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 55.632102 KDa
SequenceString: GLPWYRVHTV VLNDPGRLLS VHIMHTALVS GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWSIS GGTVTNPGI WSYEGVAGAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L YGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLLS VHIMHTALVS GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWSIS GGTVTNPGI WSYEGVAGAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L YGPGIWVS DPYGLTGKVQ AVNPAWGAEG FDPFVPGGIA SHHIAAGTLG ILAGLFHLSV RPPQRLYKGL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDQG YFQQEIYRRV SDGLAENLSL SEAWSKIPEK LAFYDYIGNN PAK GGLFRA GSMDNGDGIA VGWLGHPIFR DKEGRELFVR RMPTFFETFP VVLVDEEGIV RADVPFRRAE SKYSVEQVGV TVEF YGGEL NGVSYSDPAT VKKYARRSQL GEIFELDRAT LKSDGVFRSS PRGWFTFGHA TFALLFFFGH IWHGARTLFR DVFAG IDPD LDAQVEFGTF QKVGDPTTR

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #6: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 49.289438 KDa
SequenceString: AGRDQETTGF AWWAGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVA HFVPEKPMYE QGLILLPHLA TLGWGVGPGG EVLDTFPYF VSGVLHLISS AVLGFGGIYH ALLGPETLEE SFPFFGYVWK DRNKMTTILG IHLILLGIGA FLLVLKALYF G GIYDTWAP ...String:
AGRDQETTGF AWWAGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVA HFVPEKPMYE QGLILLPHLA TLGWGVGPGG EVLDTFPYF VSGVLHLISS AVLGFGGIYH ALLGPETLEE SFPFFGYVWK DRNKMTTILG IHLILLGIGA FLLVLKALYF G GIYDTWAP GGGDVRKITN LTLSPGVIFG YLLKSPFGGE GWIVSVDDLE DIIGGHVWLG FICVFGGIWH ILTKPFAWAR RA FVWSGEA YLSYSLGALS VFGFIACCFV WFNNTAYPSE FYGPTGPEAS QAQAFTFLVR DQRLGANVGS AQGPTGLGKY LMR SPTGEV IFGGETMRFW DLRAPWLEPL RGPNGLDLSR LKKDIQPWQE RRSAEYMTHA PLGSLNSVGG VATEINAVNY VSPR SWLAT SHFVLGFFFF VGHLWHAGRA RAAAAGFEKG IDRDLEPVLY MTPLN

UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #7: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 38.268645 KDa
SequenceString: NDLFDIMDDW LRRDRFVFVG WSGLLLFPCA YFALGGWFTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSLAHSLLL LWGPEAQGD FTRWCQLGGL WTFVALHGAF ALIGFMLRQF ELARSVQLRP YNAISFSGPI AVFVSVFLIY PLGQSGWFFA P SFGVAAIF ...String:
NDLFDIMDDW LRRDRFVFVG WSGLLLFPCA YFALGGWFTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSLAHSLLL LWGPEAQGD FTRWCQLGGL WTFVALHGAF ALIGFMLRQF ELARSVQLRP YNAISFSGPI AVFVSVFLIY PLGQSGWFFA P SFGVAAIF RFILFFQGFH NWTLNPFHMM GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ AEETYSMVTA NR FWSQIFG VAFSNKRWLH FFMLFVPVTG LWMSAIGVVG LALNLRAYDF VSQEIRAAED PEFETFYTKN ILLNEGIRAW MAA QDQPHE NLIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #8: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 8.65469 KDa
SequenceString:
RSFADIITSI RYWVIHSITI PSLFIAGWLF VSTGLAYDVF GSPRPNEYFT ESRQGIPLIT DRFDSLEQLD EFSRS

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #9: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 4.142866 KDa
SequenceString:
DRTYPIFTVR WLAVHGLAVP TVFFLGSISA MQFIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #10: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 6.472638 KDa
SequenceString:
GPRQTRVGNL LKPLNSEYGK VAPGWGTTPF MGVAMALFAV FLSIILEIYN SSVLLDGILM

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #11: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.912664 KDa
SequenceString:
MLTLKLFVYT VVIFFVSLFI FGFLSNDPGR NPGR

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #12: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.58621 KDa
SequenceString:
GRIPLWLIGT VTGIAVIGLI GVFFYGSYSG LGSSL

UniProtKB: Photosystem II reaction center protein J

+
Macromolecule #13: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 4.273128 KDa
SequenceString:
KLPEAYAIFN PIVDFMPVIP VLFFLLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #14: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 4.366904 KDa
SequenceString:
TQSNPNEQNV ELNRTSLYWG LLLIFVLAVL FSNYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #15: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 15 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.668451 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQN

UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #16: 33 kDa subunit of oxygen evolving system of photosystem II

MacromoleculeName: 33 kDa subunit of oxygen evolving system of photosystem II
type: protein_or_peptide / ID: 16 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 26.609848 KDa
SequenceString: EGVPRRLTFD EIQSKTYMEV KGTGTANQCP TVEGGVDSFA FKAGKYNMKK FCLEPTSFTV KAEGVAKNAP PEFQKTKLMT RLTYTLDEI EGPLEVSSDG TIKFEEKDGI DYAAVTVQLP GGERVPFLFT IKNLVATGKP ESFGGPFLVP SYRGSSFLDP K GRGGSTGY ...String:
EGVPRRLTFD EIQSKTYMEV KGTGTANQCP TVEGGVDSFA FKAGKYNMKK FCLEPTSFTV KAEGVAKNAP PEFQKTKLMT RLTYTLDEI EGPLEVSSDG TIKFEEKDGI DYAAVTVQLP GGERVPFLFT IKNLVATGKP ESFGGPFLVP SYRGSSFLDP K GRGGSTGY DNAVALPAGG RGDEEELAKE NVKNASSSTG NITLSVTKSK PETGEVIGVF ESVQPSDTDL GAKVPKDVKI QG VWYAQLE S

UniProtKB: 33 kDa subunit of oxygen evolving system of photosystem II

+
Macromolecule #17: 23 kDa subunit of oxygen evolving system of photosystem II

MacromoleculeName: 23 kDa subunit of oxygen evolving system of photosystem II
type: protein_or_peptide / ID: 17 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 20.122322 KDa
SequenceString:
AYGEAANVFG KPKTNTEFIA YSGEGFKLLI PSKWNPSKER EFPGQVLRYE DNFDANSNVS VIINPTTKKT ITEFGSPEEF LAQVDFLLG KQAYSGKTDS EGGFESDAVA TANILESSAP VVGGKQYYSV TVLTRTADGD EGGKHQLITA TVNDGKLYIC K AQAGDKRW FKGARKFVES AASSFSVA

UniProtKB: 23 kDa subunit of oxygen evolving system of photosystem II

+
Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 25.938283 KDa
SequenceString: RPLWFPGAVA PDYLDGSLVG DYGFDPFGLG KPAEYLQFEL DSLDQNLAKN NAGEIIGTRF ETGEVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALSVEWLTGV TWQDAGKVEL VDGSSYLGQP LPFSISTLIW IEVLVIGYIE FQRNAELDPE K RLYPGGSY ...String:
RPLWFPGAVA PDYLDGSLVG DYGFDPFGLG KPAEYLQFEL DSLDQNLAKN NAGEIIGTRF ETGEVKSTPF QPYTEVFGLQ RFRECELIH GRWAMLATLG ALSVEWLTGV TWQDAGKVEL VDGSSYLGQP LPFSISTLIW IEVLVIGYIE FQRNAELDPE K RLYPGGSY FDPLGLASDP EKKERLQLAE IKHARLAMVA FLGFAVQAAA TGKGPLNNWA THLSDPLHTT IFDTFS

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 23.719938 KDa
SequenceString: IGDELAKWYG PDRRIFLPEG LLDRSEVPDY LNGEVPGDYG YDPFGLSKKP EDFSKYQAYE LIHARWAMLG AAGFIIPEAC NKFGANCGP EAVWFKTGAL LLDGNTLNYF GNSIPINLIV AVAAEVVLVG GAEYYRIING LDLEDKLHPG GPFDPLGLAS D PDQAALLK ...String:
IGDELAKWYG PDRRIFLPEG LLDRSEVPDY LNGEVPGDYG YDPFGLSKKP EDFSKYQAYE LIHARWAMLG AAGFIIPEAC NKFGANCGP EAVWFKTGAL LLDGNTLNYF GNSIPINLIV AVAAEVVLVG GAEYYRIING LDLEDKLHPG GPFDPLGLAS D PDQAALLK VKEIKNGRLA MFSMLGFFIQ AYVTGEGPVE NLSKHLSDPF GNNLLTVISG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #20: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 20 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.692472 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKVP TK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #21: Os02g0581100 protein

MacromoleculeName: Os02g0581100 protein / type: protein_or_peptide / ID: 21 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.009631 KDa
SequenceString:
VKRGTPEAKK KYAQICVTMP TAKVCHN

UniProtKB: Os02g0581100 protein

+
Macromolecule #22: Photosystem II 10 kDa polypeptide, chloroplastic

MacromoleculeName: Photosystem II 10 kDa polypeptide, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 10.238624 KDa
SequenceString:
AKKAKKIQTS QPYGPAGGVV FKEGVDASGR VAKGKGLYQF SNKYGANVDG YSPIYTPEEW SSTGDVYVGG KAGLLLWAIT LAGILVGGA ILVYNTSALA

UniProtKB: Photosystem II 10 kDa polypeptide, chloroplastic

+
Macromolecule #23: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 5.866499 KDa
SequenceString:
LVDERMSTEG TGLSLGLSNN LLGWILLGVF GLIWSLYTIY TSDLEEDEES GGLS

UniProtKB: Photosystem II reaction center W protein, chloroplastic

+
Macromolecule #24: Os07g0673550 protein

MacromoleculeName: Os07g0673550 protein / type: protein_or_peptide / ID: 24 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.927654 KDa
SequenceString:
GSLTPSLKNF LLSIVSGGVV LVAIVGAVVA VSNFDPVKR

UniProtKB: Os07g0673550 protein

+
Macromolecule #25: cDNA clone:001-024-H10, full insert sequence

MacromoleculeName: cDNA clone:001-024-H10, full insert sequence / type: protein_or_peptide / ID: 25 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 3.932662 KDa
SequenceString:
DNRGLALLLP IAPAIAWVLY NILQPALNQL NRMRS

UniProtKB: cDNA clone:001-024-H10, full insert sequence

+
Macromolecule #26: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 26 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 6.582766 KDa
SequenceString:
MTIAFQLAVF ALIVTSSVLV ISVPLVFASP DGWSNNKNVV FSGTSLWIGL VFLVAILNSL IS

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #27: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 27 / Number of copies: 4 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.375 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

21wv
PDB Unreleased entry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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