[English] 日本語
Yorodumi
- EMDB-13078: Structure of C2S2M2-type Photosystem supercomplex from Arabidopsi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13078
TitleStructure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)
Map data
Sample
  • Complex: Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type)
    • Complex: CP24-LHCII (M-trimer)
      • Protein or peptide: x 3 types
    • Complex: LHCII S-trimer
      • Protein or peptide: x 3 types
    • Complex: CP29
    • Complex: CP26
      • Protein or peptide: x 1 types
    • Complex: Photosystem II core complex (dimer)
      • Protein or peptide: x 16 types
  • Ligand: x 19 types
KeywordsOxidoreductase / Complex / PHOTOSYNTHESIS
Function / homology
Function and homology information


photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / plastid thylakoid membrane / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule / response to high light intensity ...photoinhibition / photosynthesis, light harvesting in photosystem II / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / plastid thylakoid membrane / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / vacuolar transport / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast thylakoid lumen / apoplast / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / response to abscisic acid / oxygen evolving activity / photosystem II stabilization / chloroplast envelope / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / poly(U) RNA binding / chloroplast stroma / plastid / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / response to light stimulus / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / endoplasmic reticulum / 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 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 5kDa protein, chloroplastic / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / 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. / : / 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
(thale cress) hypothetical protein / 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 K / Photosystem II reaction center protein Z ...(thale cress) hypothetical protein / 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 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 / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsGraca AT / Hall M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Other privateCarl Trygger Sweden
Citation
Journal: Sci Rep / Year: 2021
Title: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.
Authors: André T Graça / Michael Hall / Karina Persson / Wolfgang P Schröder /
Abstract: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the ...In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated MnCaO-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD
History
DepositionJun 11, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7oui
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oui
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13078.png

Downloads & links

-
Map

FileDownload / File: emd_13078.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-19.496286000000001 - 33.681809999999999
Average (Standard dev.)-0.0038570869 (±0.9759321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-19.49633.682-0.004

-
Supplemental data

-
Sample components

+
Entire : Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...

EntireName: Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type)
Components
  • Complex: Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type)
    • Complex: CP24-LHCII (M-trimer)
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein 3, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Complex: LHCII S-trimer
      • Protein or peptide: Chlorophyll a-b binding protein 1, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein CP29.1, chloroplastic
      • Protein or peptide: Photosystem II 5 kDa protein, chloroplastic
    • Complex: CP29
    • Complex: CP26
      • Protein or peptide: Chlorophyll a-b binding protein CP26, chloroplastic
    • Complex: Photosystem II core complex (dimer)
      • 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 (PsbF)
      • 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 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: Photosystem II reaction center protein T
      • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
      • Protein or peptide: (thale cress) hypothetical protein
      • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • 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: 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: Digitonin
  • Ligand: BICARBONATE ION
  • Ligand: FE (II) ION
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • 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
  • Ligand: water

+
Supramolecule #1: Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...

SupramoleculeName: Photosystem II - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

+
Supramolecule #2: CP24-LHCII (M-trimer)

SupramoleculeName: CP24-LHCII (M-trimer) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

+
Supramolecule #3: LHCII S-trimer

SupramoleculeName: LHCII S-trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #21-#23
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

+
Supramolecule #4: CP29

SupramoleculeName: CP29 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #22
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

+
Supramolecule #5: CP26

SupramoleculeName: CP26 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #20
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

+
Supramolecule #6: Photosystem II core complex (dimer)

SupramoleculeName: Photosystem II core complex (dimer) / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #4-#19
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype / Organ: Leaf / Organelle: Chloroplast / Location in cell: Thylakoid Membrane

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.193934 KDa
SequenceString: MAASTMALSS PALTGKAVKL SPAASEVFGT GRITMRKASK PTGPSGSPWY GSDRVKYLGP FSGEPPSYLT GEFPGDYGWD TAGLSADPE TFARNRELEV IHSRWAMLGA LGCVFPELLA RNGVKFGEAV WFKAGSQIFS DGGLDYLGNP SLVHAQSILA I WATQVILM ...String:
MAASTMALSS PALTGKAVKL SPAASEVFGT GRITMRKASK PTGPSGSPWY GSDRVKYLGP FSGEPPSYLT GEFPGDYGWD TAGLSADPE TFARNRELEV IHSRWAMLGA LGCVFPELLA RNGVKFGEAV WFKAGSQIFS DGGLDYLGNP SLVHAQSILA I WATQVILM GAVEGYRVAG DGPLGEAEDL LYPGGSFDPL GLATDPEAFA ELKVKELKNG RLAMFSMFGF FVQAIVTGKG PL ENLADHL ADPVNNNAWA FATNFVPGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #2: Chlorophyll a-b binding protein 3, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 3, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.45299 KDa
SequenceString: ASSFNPLRDV VSLGSPKYTM GNDLWYGPDR VKYLGPFSVQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGAFGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQVILMGLVE GFRINGLDGV G EGNDLYPG ...String:
ASSFNPLRDV VSLGSPKYTM GNDLWYGPDR VKYLGPFSVQ TPSYLTGEFP GDYGWDTAGL SADPEAFAKN RALEVIHGRW AMLGAFGCI TPEVLQKWVR VDFKEPVWFK AGSQIFSEGG LDYLGNPNLV HAQSILAVLG FQVILMGLVE GFRINGLDGV G EGNDLYPG GQYFDPLGLA DDPVTFAELK VKEIKNGRLA MFSMFGFFVQ AIVTGKGPLE NLLDHLDNPV ANNAWAFATK FA PGA

UniProtKB: Chlorophyll a-b binding protein 3, 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.198287 KDa
SequenceString: AAAAAQPKKS WIPAVKGGGN FLDPEWLDGS LPGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMAAVLGI FVGQAWSGVA WFEAGAQPD AIAPFSFGSL LGTQLLLMGW VESKRWVDFF NPDSQSVEWA TPWSKTAENF ANYTGDQGYP GGRFFDPLGL A GKNRDGVY ...String:
AAAAAQPKKS WIPAVKGGGN FLDPEWLDGS LPGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMAAVLGI FVGQAWSGVA WFEAGAQPD AIAPFSFGSL LGTQLLLMGW VESKRWVDFF NPDSQSVEWA TPWSKTAENF ANYTGDQGYP GGRFFDPLGL A GKNRDGVY EPDFEKLERL KLAEIKHSRL AMVAMLIFYF EAGQGKTPLG ALGL

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: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.830082 KDa
SequenceString: TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS ...String:
TAILERRESE SLWGRFCNWI TSTENRLYIG WFGVLMIPTL LTATSVFIIA FIAAPPVDID GIREPVSGSL LYGNNIISGA IIPTSAAIG LHFYPIWEAA SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP VAAATAVFLI Y PIGQGSFS DGMPLGISGT FNFMIVFQAE HNILMHPFHM LGVAGVFGGS LFSAMHGSLV TSSLIRETTE NESANEGYRF GQ EEETYNI VAAHGYFGRL IFQYASFNNS RSLHFFLAAW PVVGIWFTAL GISTMAFNLN GFNFNQSVVD SQGRVINTWA DII NRANLG MEVMHERNAH NFPLDLAAVE APSTNG

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: 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 #6: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 50.086324 KDa
SequenceString: TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF ...String:
TLFNGTLALA GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGG EVIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGVGAF L LVFKALYF GGVYDTWAPG GGDVRKITNL TLSPSVIFGY LLKSPFGGEG WIVSVDDLED IIGGHVWLGS ICIFGGIWHI LT KPFAWAR RALVWSGEAY LSYSLAALSV CGFIACCFVW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVGSA QGP TGLGKY LMRSPTGEVI FGGETMRFWD LRAPWLEPLR GPNGLDLSRL KKDIQPWQER RSAEYMTHAP LGSLNSVGGV ATEI NAVNY VSPRSWLSTS HFVLGFFLFV GHLWHAGRAR AAAAGFEKGI DRDFEPVLSM TPLN

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: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 39.444082 KDa
SequenceString: TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF ...String:
TIALGKFTKD EKDLFDIMDD WLRRDRFVFV GWSGLLLFPC AYFALGGWFT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLFVPVT GLWMSALGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ENLIFPEEVL PRGNAL

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: 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 #9: Cytochrome b559 subunit beta (PsbF)

MacromoleculeName: Cytochrome b559 subunit beta (PsbF) / type: protein_or_peptide / ID: 9 / 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 #10: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.575691 KDa
SequenceString:
ATQTVEDSSR SGPRSTTVGK LLKPLNSEYG KVAPGWGTTP LMGVAMALFA VFLSIILEIY NSSVLLDGIS VN

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: 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 #12: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.239112 KDa
SequenceString:
KLPEAYAFLN PIVDVMPVIP LFFLLLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #13: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 13 / 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 #14: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 14 / 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 #15: Oxygen-evolving enhancer protein 1-1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1-1, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.594639 KDa
SequenceString: EGAPKRLTYD EIQSKTYMEV KGTGTANQCP TIDGGSETFS FKPGKYAGKK FCFEPTSFTV KADSVSKNAP PEFQNTKLMT RLTYTLDEI EGPFEVASDG SVNFKEEDGI DYAAVTVQLP GGERVPFLFT VKQLDASGKP DSFTGKFLVP SYRGSSFLDP K GRGGSTGY ...String:
EGAPKRLTYD EIQSKTYMEV KGTGTANQCP TIDGGSETFS FKPGKYAGKK FCFEPTSFTV KADSVSKNAP PEFQNTKLMT RLTYTLDEI EGPFEVASDG SVNFKEEDGI DYAAVTVQLP GGERVPFLFT VKQLDASGKP DSFTGKFLVP SYRGSSFLDP K GRGGSTGY DNAVALPAGG RGDEEELVKE NVKNTAASVG EITLKVTKSK PETGEVIGVF ESLQPSDTDL GAKVPKDVKI QG VWYGQLE

UniProtKB: Oxygen-evolving enhancer protein 1-1, 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 reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.036749 KDa
SequenceString:
LVDERMSTEG TGLPFGLSNN LLGWILFGVF GLIWTFFFVY TSSLEEDEES GLSL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

+
Macromolecule #18: (thale cress) hypothetical protein

MacromoleculeName: (thale cress) hypothetical protein / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.186916 KDa
SequenceString:
AGSGISPSLK NFLLSIASGG LVLTVIIGVV VGVSNFDPVK RT

UniProtKB: (thale cress) hypothetical protein

+
Macromolecule #19: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 19 / 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 #20: Chlorophyll a-b binding protein CP26, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP26, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.232754 KDa
SequenceString: SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE ...String:
SKAVSETSDE LAKWYGPDRR IFLPDGLLDR SEIPEYLNGE VAGDYGYDPF GLGKKPENFA KYQAFELIHA RWAMLGAAGF IIPEALNKY GANCGPEAVW FKTGALLLDG NTLNYFGKNI PINLVLAVVA EVVLLGGAEY YRITNGLDFE DKLHPGGPFD P LGLAKDPE QGALLKVKEI KNGRLAMFAM LGFFIQAYVT GEGPVENLAK HLSDPFGNNL LTVIAGTAER APTL

UniProtKB: Chlorophyll a-b binding protein CP26, chloroplastic

+
Macromolecule #21: Chlorophyll a-b binding protein 1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.885072 KDa
SequenceString: RKTVAKPKGP SGSPWYGSDR VKYLGPFSGE SPSYLTGEFP GDYGWDTAGL SADPETFARN RELEVIHSRW AMLGALGCVF PELLARNGV KFGEAVWFKA GSQIFSDGGL DYLGNPSLVH AQSILAIWAT QVILMGAVEG YRVAGNGPLG EAEDLLYPGG S FDPLGLAT ...String:
RKTVAKPKGP SGSPWYGSDR VKYLGPFSGE SPSYLTGEFP GDYGWDTAGL SADPETFARN RELEVIHSRW AMLGALGCVF PELLARNGV KFGEAVWFKA GSQIFSDGGL DYLGNPSLVH AQSILAIWAT QVILMGAVEG YRVAGNGPLG EAEDLLYPGG S FDPLGLAT DPEAFAELKV KELKNGRLAM FSMFGFFVQA IVTGKGPIEN LADHLADPVN NNAWAFATNF VPGK

UniProtKB: Chlorophyll a-b binding protein 1, chloroplastic

+
Macromolecule #22: Chlorophyll a-b binding protein CP29.1, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP29.1, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.302855 KDa
SequenceString: AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ...String:
AAPKKSAKKT VTTDRPLWYP GAISPDWLDG SLVGDYGFDP FGLGKPAEYL QFDIDSLDQN LAKNLAGDVI GTRTEAADAK STPFQPYSE VFGIQRFREC ELIHGRWAML ATLGALSVEW LTGVTWQDAG KVELVDGSSY LGQPLPFSIS TLIWIEVLVI G YIEFQRNA ELDSEKRLYP GGKFFDPLGL AADPEKTAQL QLAEIKHARL AMVAFLGFAV QAAATGKGPL NNWATHLSDP LH TTIIDTF SSS

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

+
Macromolecule #23: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.17881 KDa
SequenceString:
EPKRGTEAAK KKYAQVCVTM PTAKICRY

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

+
Macromolecule #24: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 24 / Number of copies: 60 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 162 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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

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

+
Macromolecule #27: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 27 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #28: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 28 / Number of copies: 22 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #29: 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: 29 / Number of copies: 8 / 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 #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 30 / Number of copies: 12 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #31: 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: 31 / Number of copies: 4 / 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 #32: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 32 / Number of copies: 22 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

+
Macromolecule #33: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

+
Macromolecule #34: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 34 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #36: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 36 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #37: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 37 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #38: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 38 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #39: (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: 39 / 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 #40: (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: 40 / 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 #41: (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: 41 / Number of copies: 2 / 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

+
Macromolecule #42: water

MacromoleculeName: water / type: ligand / ID: 42 / Number of copies: 139 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Component - Name: HEPES-KOH / Details: 10mM HEPES-KOH pH7.5 + 0.01% (w/v) digitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 50 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -5 Wait time 1s Blotting time 5s.
DetailsIndicated sample concentration based on Chlorophyll measurement.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 12227 / Average electron dose: 1.49 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.15) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5mdx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 100712
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15)

+
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