[English] 日本語
Yorodumi
- EMDB-63167: Cryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63167
TitleCryo-EM structure of Lhcb4.1-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Map data
Sample
  • Complex: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
    • Protein or peptide: x 21 types
  • Protein or peptide: x 1 types
  • Ligand: x 15 types
KeywordsPhotosystem II / light harvesting / photoacclimation / stress-induced antennae / cryo-EM / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / response to desiccation / photoinhibition / nonphotochemical quenching / cellular response to abscisic acid stimulus / cellular response to water deprivation / response to red light / plastid thylakoid membrane ...photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / response to desiccation / photoinhibition / nonphotochemical quenching / cellular response to abscisic acid stimulus / cellular response to water deprivation / response to red light / plastid thylakoid membrane / chloroplast stromal thylakoid / response to low light intensity stimulus / thylakoid lumen / plastoglobule / regulation of stomatal closure / response to high light intensity / thylakoid membrane / response to far red light / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / vacuolar transport / thylakoid / photosynthesis, light harvesting / chloroplast thylakoid lumen / apoplast / photosystem II oxygen evolving complex / photosystem II assembly / response to fructose / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / chloroplast envelope / photosystem II / plant-type vacuole / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / photosystem II / response to herbicide / poly(U) RNA binding / plastid / chloroplast stroma / chlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / positive regulation of reactive oxygen species biosynthetic process / : / 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 / mitochondrion / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / 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 PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein 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 reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / 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 / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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
(thale cress) hypothetical protein / Chlorophyll a-b binding protein 2, 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 ...(thale cress) hypothetical protein / Chlorophyll a-b binding protein 2, 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 / Chlorophyll a-b binding protein 2.2, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhou Q / Caferri R / Shan JY / Amelii A / Bassi R / Liu ZF
Funding supportEuropean Union, China, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2025
Title: A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana.
Authors: Roberto Caferri / Qian Zhou / Luca Dall'Osto / Antonello Amelii / Jianyu Shan / Zhenfeng Liu / Roberto Bassi /
Abstract: Photosystem II (PSII) is the pigment-protein complex catalysing light-induced water oxidation. In Arabidopsis thaliana, it includes three Lhcb4-6 proteins linking the core complex to peripheral ...Photosystem II (PSII) is the pigment-protein complex catalysing light-induced water oxidation. In Arabidopsis thaliana, it includes three Lhcb4-6 proteins linking the core complex to peripheral trimeric antennae. While Lhcb5 and Lhcb6 are encoded by single genes, Lhcb4 is encoded by three isoforms: Lhcb4.1 and Lhcb4.2, constitutively expressed, and Lhcb4.3 (Lhcb8), which accumulates under prolonged abiotic stress. Lhcb8 substitutes for Lhcb4, preventing Lhcb6 accumulation and resulting in a smaller PSII with high quantum yield. Cryo-electron microscopy reveals that Lhcb8 has a shorter carboxy-terminal domain, lacks two chlorophylls, and interacts more tightly with the PSII core, inducing structural changes in the PSII antenna system, ultimately inhibiting the formation of PSII arrays and favouring plastoquinone diffusion. We suggest that dynamic Lhcb4 vs Lhcb8 expression allows for PSII acclimation to contrasting light conditions, offering the potential for engineering crops with improved light use efficiency.
History
DepositionJan 16, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63167.png

Downloads & links

-
Map

FileDownload / File: emd_63167.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-22.323090000000001 - 37.375613999999999
Average (Standard dev.)0.01306359 (±1.094894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from ...

EntireName: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Components
  • Complex: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
    • 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 alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Chlorophyll a-b binding protein 2, chloroplastic
    • 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 K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Oxygen-evolving enhancer protein 1-1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein CP29.1, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II 5 kDa protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: (thale cress) hypothetical protein
    • Protein or peptide: Chlorophyll a-b binding protein 2.2, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein Z
  • Protein or peptide: Chlorophyll a-b binding protein CP26, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: FE (II) ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BICARBONATE ION
  • Ligand: 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
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (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
  • Ligand: (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

+
Supramolecule #1: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from ...

SupramoleculeName: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Arabidopsis thaliana (thale cress)

+
Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.961277 KDa
SequenceString: MTAILERRES ESLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAI GLHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL I YPIGQGSF ...String:
MTAILERRES ESLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAI GLHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGIWFTA LGISTMAFNL NGFNFNQSVV DSQGRVINTW ADI INRANL GMEVMHERNA HNFPLDLAAV EAPSTNG

UniProtKB: Photosystem II protein D1

+
Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.091824 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLL AVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG LWSYEGVAGA HIVFSGLCFL AAIWHWVYWD LEIFCDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLL AVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWNI TGGTITNPG LWSYEGVAGA HIVFSGLCFL AAIWHWVYWD LEIFCDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV SDPYGLTGKV QPVNPAWGVE GFDPFVPGGI ASHHIAAGTL GILAGLFHLS VRPPQRLYKG LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSATTPIEL FGPTRYQWDQ GYFQQEIYRR VSAGLAENQS LSEAWAKIPE KLAFYDYIGN NPA KGGLFR AGSMDNGDGI AVGWLGHPVF RNKEGRELFV RRMPTFFETF PVVLVDGDGI VRADVPFRRA ESKYSVEQVG VTVE FYGGE LNGVSYSDPA TVKKYARRAQ LGEIFELDRA TLKSDGVFRS SPRGWFTFGH ASFALLFFFG HIWHGARTLF RDVFA GIDP DLDAQVEFGA FQKLGDPTTK RQAV

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 51.9155 KDa
SequenceString: MKTLYSLRRF YHVETLFNGT LALAGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL ...String:
MKTLYSLRRF YHVETLFNGT LALAGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL GVGAFLLVFK ALYFGGVYDT WAPGGGDVRK ITNLTLSPSV IFGYLLKSPF GGEGWIVSVD DLEDIIGGHV WL GSICIFG GIWHILTKPF AWARRALVWS GEAYLSYSLA ALSVCGFIAC CFVWFNNTAY PSEFYGPTGP EASQAQAFTF LVR DQRLGA NVGSAQGPTG LGKYLMRSPT GEVIFGGETM RFWDLRAPWL EPLRGPNGLD LSRLKKDIQP WQERRSAEYM THAP LGSLN SVGGVATEIN AVNYVSPRSW LSTSHFVLGF FLFVGHLWHA GRARAAAAGF EKGIDRDFEP VLSMTPLN

UniProtKB: Photosystem II CP43 reaction center protein

+
Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.575281 KDa
SequenceString: MTIALGKFTK DEKDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHS LLLLWGPEAQ GDFTRWCQLG GLWAFVALHG AFALIGFMLR QFELARSVQL RPYNAIAFSG PIAVFVSVFL I YPLGQSGW ...String:
MTIALGKFTK DEKDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHS LLLLWGPEAQ GDFTRWCQLG GLWAFVALHG AFALIGFMLR QFELARSVQL RPYNAIAFSG PIAVFVSVFL I YPLGQSGW FFAPSFGVAA IFRFILFFQG FHNWTLNPFH MMGVAGVLGA ALLCAIHGAT VENTLFEDGD GANTFRAFNP TQ AEETYSM VTANRFWSQI FGVAFSNKRW LHFFMLFVPV TGLWMSALGV VGLALNLRAY DFVSQEIRAA EDPEFETFYT KNI LLNEGI RAWMAAQDQP HENLIFPEEV LPRGNAL

UniProtKB: Photosystem II D2 protein

+
Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.393501 KDa
SequenceString:
MSGSTGERSF ADIITSIRYW VIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTESR QGIPLITGRF DSLEQLDEFS RSF

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.428228 KDa
SequenceString:
MTIDRTYPIF TVRWLAVHGL AVPTVSFLGS ISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #7: Chlorophyll a-b binding protein 2, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2, chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.250984 KDa
SequenceString: MAASTMALSS PAFAGKAVNL SPAASEVLGS GRVTMRKTVA KPKGPSGSPW YGSDRVKYLG PFSGESPSYL TGEFPGDYGW DTAGLSADP ETFARNRELE VIHSRWAMLG ALGCVFPELL ARNGVKFGEA VWFKAGSQIF SDGGLDYLGN PSLVHAQSIL A IWATQVIL ...String:
MAASTMALSS PAFAGKAVNL SPAASEVLGS GRVTMRKTVA KPKGPSGSPW YGSDRVKYLG PFSGESPSYL TGEFPGDYGW DTAGLSADP ETFARNRELE VIHSRWAMLG ALGCVFPELL ARNGVKFGEA VWFKAGSQIF SDGGLDYLGN PSLVHAQSIL A IWATQVIL MGAVEGYRVA GNGPLGEAED LLYPGGSFDP LGLATDPEAF AELKVKELKN GRLAMFSMFG FFVQAIVTGK GP IENLADH LADPVNNNAW AFATNFVPGK

UniProtKB: Chlorophyll a-b binding protein 2, chloroplastic

+
Macromolecule #8: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.706887 KDa
SequenceString:
MATQTVEDSS RSGPRSTTVG KLLKPLNSEY GKVAPGWGTT PLMGVAMALF AVFLSIILEI YNSSVLLDGI SVN

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #9: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.170891 KDa
SequenceString:
MLTLKLFVYT VVIFFVSLFI FGFLSNDPGR NPGREE

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #10: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.117832 KDa
SequenceString:
MADTTGRIPL WVIGTVAGIL VIGLIGIFFY GSYSGLGSSL

UniProtKB: Photosystem II reaction center protein J

+
Macromolecule #11: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.977381 KDa
SequenceString:
MLNIFNLICI FFNSTLFSST FLVAKLPEAY AFLNPIVDVM PVIPLFFLLL AFVWQAAVSF R

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #12: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.471075 KDa
SequenceString:
MTQSNPNEQS VELNRTSLYW GLLLIFVLAV LFSNYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #13: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.783538 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQND

UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #14: Oxygen-evolving enhancer protein 1-1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1-1, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 35.180262 KDa
SequenceString: MAASLQSTAT FLQSAKIATA PSRGSSHLRS TQAVGKSFGL ETSSARLTCS FQSDFKDFTG KCSDAVKIAG FALATSALVV SGASAEGAP KRLTYDEIQS KTYMEVKGTG TANQCPTIDG GSETFSFKPG KYAGKKFCFE PTSFTVKADS VSKNAPPEFQ N TKLMTRLT ...String:
MAASLQSTAT FLQSAKIATA PSRGSSHLRS TQAVGKSFGL ETSSARLTCS FQSDFKDFTG KCSDAVKIAG FALATSALVV SGASAEGAP KRLTYDEIQS KTYMEVKGTG TANQCPTIDG GSETFSFKPG KYAGKKFCFE PTSFTVKADS VSKNAPPEFQ N TKLMTRLT YTLDEIEGPF EVASDGSVNF KEEDGIDYAA VTVQLPGGER VPFLFTVKQL DASGKPDSFT GKFLVPSYRG SS FLDPKGR GGSTGYDNAV ALPAGGRGDE EELVKENVKN TAASVGEITL KVTKSKPETG EVIGVFESLQ PSDTDLGAKV PKD VKIQGV WYGQLE

UniProtKB: Oxygen-evolving enhancer protein 1-1, chloroplastic

+
Macromolecule #15: Chlorophyll a-b binding protein CP29.1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP29.1, chloroplastic / type: protein_or_peptide / ID: 15
Details: A 4*glycine followed by a 6*HisTAG was added to the C-terminal of the protein
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 32.227412 KDa
Recombinant expressionOrganism: Arabidopsis thaliana (thale cress)
SequenceString: MAATSAAAAA ASSIMGTRVA PGIHPGSGRF TAVFGFGKKK AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEY LQFDIDSLDQ NLAKNLAGDV IGTRTEAADA KSTPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW L TGVTWQDA ...String:
MAATSAAAAA ASSIMGTRVA PGIHPGSGRF TAVFGFGKKK AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEY LQFDIDSLDQ NLAKNLAGDV IGTRTEAADA KSTPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW L TGVTWQDA GKVELVDGSS YLGQPLPFSI STLIWIEVLV IGYIEFQRNA ELDSEKRLYP GGKFFDPLGL AADPEKTAQL QL AEIKHAR LAMVAFLGFA VQAAATGKGP LNNWATHLSD PLHTTIIDTF SSSGGGGHHH HHH

UniProtKB: Chlorophyll a-b binding protein CP29.1, chloroplastic

+
Macromolecule #16: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.825642 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKIS TKK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #17: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.042852 KDa
SequenceString:
MASMTMTATF FPAVAKVPSA TGGRRLSVVR ASTSDNTPSL EVKEQSSTTM RRDLMFTAAA AAVCSLAKVA MAEEEEPKRG TEAAKKKYA QVCVTMPTAK ICRY

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

+
Macromolecule #18: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.685823 KDa
SequenceString:
MASFTASAST VSAARPALLL KPTVAISAPV LGLPPMGKKK GGVRCSMETK QGNVSVMGAG VSAAATAALT AVMSNPAMAL VDERMSTEG TGLPFGLSNN LLGWILFGVF GLIWTFFFVY TSSLEEDEES GLSL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

+
Macromolecule #19: (thale cress) hypothetical protein

MacromoleculeName: (thale cress) hypothetical protein / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.826013 KDa
SequenceString:
MASTSAMSLV TPLNQTRSSP FLKPLPLKPS KALVATGGRA QRLQVKALKM DKALTGISAA ALTASMVIPE IAEAAGSGIS PSLKNFLLS IASGGLVLTV IIGVVVGVSN FDPVKRT

UniProtKB: (thale cress) hypothetical protein

+
Macromolecule #20: Chlorophyll a-b binding protein 2.2, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 2.2, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.644432 KDa
SequenceString: MATSAIQQSS FAGQTALKPS SDLIQKVGVL GGGRVTMRRT VKSTPQSIWY GPDRPKYLGP FSENTPSYLT GEYPGDYGWD TAGLSADPE TFAKNRELEV IHSRWAMLGA LGCTFPEILS KNGVKFGEAV WFKAGSQIFS EGGLDYLGNP NLIHAQSILA I WAVQVVLM ...String:
MATSAIQQSS FAGQTALKPS SDLIQKVGVL GGGRVTMRRT VKSTPQSIWY GPDRPKYLGP FSENTPSYLT GEYPGDYGWD TAGLSADPE TFAKNRELEV IHSRWAMLGA LGCTFPEILS KNGVKFGEAV WFKAGSQIFS EGGLDYLGNP NLIHAQSILA I WAVQVVLM GFIEGYRIGG GPLGEGLDPL YPGGAFDPLN LAEDPEAFSE LKVKELKNGR LAMFSMFGFF VQAIVTGKGP IE NLFDHLA DPVANNAWSY ATNFVPGK

UniProtKB: Chlorophyll a-b binding protein 2.2, chloroplastic

+
Macromolecule #21: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.569768 KDa
SequenceString:
MTIAFQLAVF ALIITSSILL ISVPVVFASP DGWSSNKNVV FSGTSLWIGL VFLVGILNSL IS

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #22: Chlorophyll a-b binding protein CP26, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP26, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 30.187576 KDa
SequenceString: MASLGVSEML GTPLNFRAVS RSSAPLASSP STFKTVALFS KKKPAPAKSK AVSETSDELA KWYGPDRRIF LPDGLLDRSE IPEYLNGEV AGDYGYDPFG LGKKPENFAK YQAFELIHAR WAMLGAAGFI IPEALNKYGA NCGPEAVWFK TGALLLDGNT L NYFGKNIP ...String:
MASLGVSEML GTPLNFRAVS RSSAPLASSP STFKTVALFS KKKPAPAKSK AVSETSDELA KWYGPDRRIF LPDGLLDRSE IPEYLNGEV AGDYGYDPFG LGKKPENFAK YQAFELIHAR WAMLGAAGFI IPEALNKYGA NCGPEAVWFK TGALLLDGNT L NYFGKNIP INLVLAVVAE VVLLGGAEYY RITNGLDFED KLHPGGPFDP LGLAKDPEQG ALLKVKEIKN GRLAMFAMLG FF IQAYVTG EGPVENLAKH LSDPFGNNLL TVIAGTAERA PTL

UniProtKB: Chlorophyll a-b binding protein CP26, chloroplastic

+
Macromolecule #23: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 23 / Number of copies: 156 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #24: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 24 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #26: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 26 / Number of copies: 6 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 27 / Number of copies: 8 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 6 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #29: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 29 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 26 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

+
Macromolecule #31: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

+
Macromolecule #32: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 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
type: ligand / ID: 32 / Number of copies: 2 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

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

+
Macromolecule #33: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 33 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #34: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 34 / Number of copies: 52 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #35: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 35 / Number of copies: 18 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

+
Macromolecule #36: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (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
type: ligand / ID: 36 / Number of copies: 10 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

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

+
Macromolecule #37: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (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
type: ligand / ID: 37 / Number of copies: 8 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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:

7oui

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67864
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