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- EMDB-54531: Universal Photosystem II Intermediate with Light-Dependent Water-... -

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Basic information

Entry
Database: EMDB / ID: EMD-54531
TitleUniversal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Pisum sativum
Map data
Sample
  • Complex: Photosystem II Intermediate
    • Protein or peptide: x 19 types
  • Ligand: x 14 types
KeywordsHigher plants / PSII / Pisum sativum / membrane protein / Cryo-EM / PHOTOSYNTHESIS / assembly intermediate / water-ferrocyanide oxido-reductase.
Function / homology
Function and homology information


photoinhibition / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide ...photoinhibition / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / poly(U) RNA binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily ...Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II protein D1 / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II reaction center protein I / Photosystem II 5 kDa protein, chloroplastic / PSII 6.1 kDa protein / Ultraviolet-B-repressible protein / Photosystem II reaction center protein K / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha ...Photosystem II reaction center protein I / Photosystem II 5 kDa protein, chloroplastic / PSII 6.1 kDa protein / Ultraviolet-B-repressible protein / Photosystem II reaction center protein K / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / 16 kDa subunit of oxygen evolving system of photosystem II / Photosystem II reaction center protein T / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesPisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsNelson N / Klaiman D / Fadeeva M / Kandiah E
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Universal Photosystem II Intermediate with Light-Dependent Water-Ferrocyanide Oxydo-reductase activity from Pisum sativum
Authors: Nelson N / Klaiman D / Fadeeva M
History
DepositionJul 24, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54531.png

Downloads & links

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Map

FileDownload / File: emd_54531.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.058739964 - 0.14679728
Average (Standard dev.)0.00016581279 (±0.004950842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 263.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54531_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54531_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem II Intermediate

EntireName: Photosystem II Intermediate
Components
  • Complex: Photosystem II Intermediate
    • 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: 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, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 2, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 3
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: PSII 6.1 kDa protein
    • Protein or peptide: Ultraviolet-B-repressible protein
    • Protein or peptide: Photosystem II 5 kDa protein, chloroplastic
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • 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: 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: BICARBONATE ION
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

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Supramolecule #1: Photosystem II Intermediate

SupramoleculeName: Photosystem II Intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 36.972074 KDa
SequenceString: ENLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEA ASVDEWLYNG GPYELIVLHF LLGVACYMGR EWELSFRLGM RPWIAVAYSA PVAAATAVFL IYPIGQGSFS D GMPLGISG ...String:
ENLWGRFCNW 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

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Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 53.157574 KDa
SequenceString: GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS ...String:
GLPWYRVHTV VLNDPGRLLS VHIMHTALVA GWAGSMALYE LAVFDPSDPV LDPMWRQGMF VIPFMTRLGI TNSWGGWNIT GGTITNPGI WSYEGVAAAH IVFSGLCFLA AIWHWVYWDL EIFCDERTGK PSLDLPKIFG IHLFLAGVAC FGFGAFHVTG L FGPGIWVS DPYGLTGRVQ SVNPAWGVDG FDPFVPGGIA SHHIAAGTLG ILAGLFHLSV RPPQRLYKGL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDQG YFQQEIYRRV GGGLVENQSL SEAWSKIPEK LAFYDYIGNN PAK GGLFRA GSMDNGDGIA VGWLGHPIFR DKEGRELFVR RMPTFFETFP VVLVDGDGIV RADVPFRRAE SKYSVEQVGV IVEF YGGEL NGVSYSDPAT VKKYARRAQL GEIFELDRAT LKSDGVFRSS PRGWFTFGHA SFALLFFFGH IWHGARTLFR DVFAG I

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 49.174273 KDa
SequenceString: GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGGE VIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGIGSF LLVFKAFYFG G IYDTWAPG ...String:
GRDQETTGFA WWAGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVAH FVPEKPMYEQ GLILLPHLAT LGWGVGPGGE VIDTFPYFV SGVLHLISSA VLGFGGIYHA LLGPETLEES FPFFGYVWKD RNKMTTILGI HLILLGIGSF LLVFKAFYFG G IYDTWAPG GGDVRKITNF TLSPSILFGY LLKSPFGGEG WIVSVDDLED IIGGHVWLGS ICILGGIWHI LTKPFAWARR AL VWSGEAY LSYSLGALAV FGFIACCFVW FNNTAYPSEF YGPTGPEASQ AQAFTFLVRD QRLGANVGSA QGPTGLGKYL MRS PTGEVI FGGETMRFWD LRAPWLEPLR GPNGLDLSRL KKDIQPWQER RSAEYMTHAP LGSLNSVGGV ATEINAVNYV SPRS WLATS HFVLGFFLFV GHLWHAGRAR AAAAGFEKGI DRDFEPVLSM TPLN

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 38.106496 KDa
SequenceString: DLFDIMDDWL RRDRFVFVGW SGLLLFPCAY FAVGGWFTGT TFVTSWYTHG LASSYLEGCN FLTAAVSTPA NSLAHSLLLL WGPEAQGDL TRWCQLGGLW TFVALHGAFG LIGFMLRQFE LARSVQLRPY NAIAFSGPIA VFVSVFLIYP LGQSGWFFAP S FGVAAIFR ...String:
DLFDIMDDWL RRDRFVFVGW SGLLLFPCAY FAVGGWFTGT TFVTSWYTHG LASSYLEGCN FLTAAVSTPA NSLAHSLLLL WGPEAQGDL TRWCQLGGLW TFVALHGAFG LIGFMLRQFE LARSVQLRPY NAIAFSGPIA VFVSVFLIYP LGQSGWFFAP S FGVAAIFR FILFFQGFHN WTLNPFHMMG VAGVLGAALL CAIHGATVEN TLFEDGDGAN TFRAFNPTQA EETYSMVTAN RF WSQIFGV AFSNKRWLHF FMLFVPVTGL WMSALGVVGL ALNLRAYDFV SQEIRAAEDP EFETFYTKNI LLNEGIRAWM ATQ DQPHEN LIFPEEVLPR GNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 8.624707 KDa
SequenceString:
RSFADIITSI RYWIIHSITI PSLFIAGWLF VSTGLAYDVF GSPRPNEYFT ETRQGIPLIT GRFDSLEQLD EFSRS

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.396035 KDa
SequenceString:
FTVRWLAVHG LAVPTVFFLG SISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 6.455607 KDa
SequenceString:
GPRRTAVGDL LKPLNSEYGK VAPGWGTTPL MGIAMALFAV FLSIILEIYN SSLLLDQISM

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.769497 KDa
SequenceString:
MLTLKLFVYT IVIFFVSLFI FGFLSNDPGR NPG

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #9: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.598264 KDa
SequenceString:
GRIPLWIIGT VAGIVVIGLI GLFFYGSYSG LGSSL

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #10: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.287155 KDa
SequenceString:
KLPEAYAFLN PIVDFMPVIP LLFFLLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #11: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.137672 KDa
SequenceString:
SNPNEQNVEL NRTSLYWGLL LIFVLAVLFS NYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #12: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.066779 KDa
SequenceString:
NILAFIATAL FILVPTAFLL IIYVKTVS

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #13: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 26.554646 KDa
SequenceString: EGAPKRLTFD EIQSKTYLEV KGTGTANQCP TIDGGVDSFS FKPGKYNAKK LCLEPTSFTV KSEGVTKNTP LAFQNTKLMT RLTYTLDEI EGPFEVSADG SVKFEEKDGI DYAAVTVQLP GGERVPFLFT IKQLVASGKP DSFSGEFLVP SYRGSSFLDP K GRGASTGY ...String:
EGAPKRLTFD EIQSKTYLEV KGTGTANQCP TIDGGVDSFS FKPGKYNAKK LCLEPTSFTV KSEGVTKNTP LAFQNTKLMT RLTYTLDEI EGPFEVSADG SVKFEEKDGI DYAAVTVQLP GGERVPFLFT IKQLVASGKP DSFSGEFLVP SYRGSSFLDP K GRGASTGY DNAVALPAGG RGDEEELGKE NNKSAASSKG KITLSVTQTK PETGEVIGVF ESIQPSDTDL GAKAPKDVKI QG VWYAQLE S

UniProtKB: Oxygen-evolving enhancer protein 1, chloroplastic

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Macromolecule #14: Oxygen-evolving enhancer protein 2, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 2, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 20.287494 KDa
SequenceString:
AYGEAANVFG KAKTNTDYLP YNGDGFKLLV PAKWNPSKER EFPGQVLRYE DNFDATSNVS VLVQTTDKKS ITDYGSPEEF LSKVDYLLG KQAFFGQTDS EGGFDTNAVA VANILESSAP VIGGKQYYNI SVLTRTADGD EGGKHQLITA TVKDGKLYIC K AQAGDKRW FKGARKFVED TASSFSVA

UniProtKB: Oxygen-evolving enhancer protein 2, chloroplastic

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Macromolecule #15: Oxygen-evolving enhancer protein 3

MacromoleculeName: Oxygen-evolving enhancer protein 3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 16.398898 KDa
SequenceString:
EAIPIKVGGP PPLSGGLPGT LNSDEARDLK LPLKERFFIQ PLAPTEAAAR TKESAKEIVA AKKFIDQKAW PFLQNDLRLR AGYLRYDLK TIISSKPKDQ KQSLKELTDK LFQDISNLDH AAKIKSPSEA EKYYAIAVST LNDVLSKIA

UniProtKB: 16 kDa subunit of oxygen evolving system of photosystem II

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Macromolecule #16: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.462189 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKVP

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #17: PSII 6.1 kDa protein

MacromoleculeName: PSII 6.1 kDa protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 5.198879 KDa
SequenceString:
LVDDRMSTEG TGLPFGLSNN LLGWILFGVF GLIWALYFIY ASGLDED

UniProtKB: PSII 6.1 kDa protein

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Macromolecule #18: Ultraviolet-B-repressible protein

MacromoleculeName: Ultraviolet-B-repressible protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.544123 KDa
SequenceString:
ATVSPSLKNF LLSIVSGGVV VTAILGAVIG VSNFDP

UniProtKB: Ultraviolet-B-repressible protein

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Macromolecule #19: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.080648 KDa
SequenceString:
EPKRGSPEAK KAYAPVCVTM PTARICRN

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

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Macromolecule #20: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 20 / Number of copies: 1 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #21: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #22: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 22 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #23: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 23 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #24: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 24 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 8 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: 1 / 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

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Macromolecule #27: 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: 27 / 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

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Macromolecule #28: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 28 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #32: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 32 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 778 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 288 K / Instrument: LEICA EM GP
DetailsChlorophyll concentration

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 24215 / Average exposure time: 2.2 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7825226
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yp7

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 323534
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: UCSF Chimera
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: PHENIX
Final 3D classificationNumber classes: 6 / Avg.num./class: 71300 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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