[English] 日本語
Yorodumi
- EMDB-39860: cryo-EM structure of PSII-LHCII megacomplex from spinach -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39860
Titlecryo-EM structure of PSII-LHCII megacomplex from spinach
Map data
Sample
  • Complex: PSII-LHCII megacomplex
    • Protein or peptide: x 28 types
  • Ligand: x 18 types
KeywordsPSII / LHCII / megacomplex / photosynthesis
Function / homology
Function and homology information


chloroplast photosystem II / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...chloroplast photosystem II / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / 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 / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / response to light stimulus / photosynthesis / cell redox homeostasis / chloroplast / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / : / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Photosystem II 5kDa protein, chloroplastic / PsbP, C-terminal / PsbP / : / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II 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
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein LOC110783121 / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP43 reaction center protein ...Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein LOC110783121 / Chlorophyll a-b binding protein, chloroplastic / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II 10 kDa polypeptide, chloroplastic / Photosystem II reaction center protein K / Oxygen-evolving enhancer protein 3, chloroplastic / Oxygen-evolving enhancer protein 2, chloroplastic / Oxygen-evolving enhancer protein 1, chloroplastic / Chlorophyll a-b binding protein CP24, chloroplastic / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II protein D1 / Photosystem II reaction center proteins PsbY, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II reaction center protein J / Photosystem II reaction center protein Z
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsShan JY / Liu ZF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2024
Title: Architecture and functional regulation of a plant PSII-LHCII megacomplex.
Authors: Jianyu Shan / Dariusz M Niedzwiedzki / Rupal S Tomar / Zhenfeng Liu / Haijun Liu /
Abstract: Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR- ...Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the CSM-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I CSM megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt ; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in Q site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.
History
DepositionApr 23, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_39860.png

Downloads & links

-
Map

FileDownload / File: emd_39860.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.35 Å/pix.
x 480 pix.
= 648. Å		1.35 Å/pix.
x 480 pix.
= 648. Å		1.35 Å/pix.
x 480 pix.
= 648. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-20.734634 - 34.286349999999999
Average (Standard dev.)-0.0043487144 (±0.986466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : PSII-LHCII megacomplex

EntireName: PSII-LHCII megacomplex
Components
  • Complex: PSII-LHCII megacomplex
    • Protein or peptide: Photosystem II 10 kDa polypeptide, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein CP24, chloroplastic
    • Protein or peptide: Photosystem II reaction center proteins PsbY, chloroplastic
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Chlorophyll a-b binding protein, 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, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 2, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 3, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II 5 kDa protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center X protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • 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: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-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: (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: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

+
Supramolecule #1: PSII-LHCII megacomplex

SupramoleculeName: PSII-LHCII megacomplex / type: complex / ID: 1 / Parent: 0
Macromolecule list: #16, #14-#15, #11, #17, #1, #28, #18-#21, #9, #22-#27, #2, #12-#13, #3-#8, #10
Source (natural)Organism: Spinacia oleracea (spinach)

+
Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 38.804152 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 HNFPLDLAAI EAPST

UniProtKB: Photosystem II protein D1

+
Macromolecule #2: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 35.207383 KDa
SequenceString: MAASLQASTT FLQPTKVASR NTLQLRSTQN VCKAFGVESA SSGGRLSLSL QSDLKELANK CVDATKLAGL ALATSALIAS GANAEGGKR LTYDEIQSKT YLEVKGTGTA NQCPTVEGGV DSFAFKPGKY TAKKFCLEPT KFAVKAEGIS KNSGPDFQNT K LMTRLTYT ...String:
MAASLQASTT FLQPTKVASR NTLQLRSTQN VCKAFGVESA SSGGRLSLSL QSDLKELANK CVDATKLAGL ALATSALIAS GANAEGGKR LTYDEIQSKT YLEVKGTGTA NQCPTVEGGV DSFAFKPGKY TAKKFCLEPT KFAVKAEGIS KNSGPDFQNT K LMTRLTYT LDEIEGPFEV SSDGTVKFEE KDGIDYAAVT VQLPGGERVP FLFTIKQLVA SGKPESFSGD FLVPSYRGSS FL DPKGRGG STGYDNAVAL PAGGRGDEEE LQKENNKNVA SSKGTITLSV TSSKPETGEV IGVFQSLQPS DTDLGAKVPK DVK IEGVWY AQLEQQ

UniProtKB: Oxygen-evolving enhancer protein 1, chloroplastic

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 31.046254 KDa
SequenceString: MASASASAAA TSSFIGTRLT EVPSNSGKVT CRFGFGAKKV AKKAQPKSGF STDRPLWYPG AKAPEYLDGS LVGDYGFDPF GLGKPAEYL QYDYDGLDQN LAKNLAGDII GTRTESADVK STSLQPYSEV FGLQRFRECE LIHGRWAMLA TLGALTVEGL T GITWQDAG ...String:
MASASASAAA TSSFIGTRLT EVPSNSGKVT CRFGFGAKKV AKKAQPKSGF STDRPLWYPG AKAPEYLDGS LVGDYGFDPF GLGKPAEYL QYDYDGLDQN LAKNLAGDII GTRTESADVK STSLQPYSEV FGLQRFRECE LIHGRWAMLA TLGALTVEGL T GITWQDAG KVELIEGSSY LGQPLPFSMT TLIWIEVLVI GYIEFQRNAE LDTEKRLYPG GTFDPLGLAS DPEKKPILQL AE IKHARLA MVGFLGFAVQ AAVTGKGPLN NWVTHLSDPL HTTILDRFL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 31.34184 KDa
SequenceString: MASVAASTAA ACLGKSELLG NSLNLRSATS APCSTPSVGP CKIVALFNFG KKAATPPAKS KAKVAVASPA DDELAKWYGP DRRIFLPDG LLDRDDIPEY LNGEVPGDYG YDPFGLGKKP EDFAKYQAFE LIHARWAMLG AAGCVIPEAF NKFGANCGPE A VWFKTGAL ...String:
MASVAASTAA ACLGKSELLG NSLNLRSATS APCSTPSVGP CKIVALFNFG KKAATPPAKS KAKVAVASPA DDELAKWYGP DRRIFLPDG LLDRDDIPEY LNGEVPGDYG YDPFGLGKKP EDFAKYQAFE LIHARWAMLG AAGCVIPEAF NKFGANCGPE A VWFKTGAL LLDGNTLNYF GKNIPINLVL AVVAEVVLLG GAEYYRITNG LDFEDKLHPG GPFDPLGLAK DPDQAALLKV KE IKNGRLA MFSMFAFFIQ AYVTGQGPVE NLSAHLSDPF GNNLLTVIGG AAERVPTL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #5: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 3.825642 KDa
SequenceString:
MEALVYTFLL VSTLGIIFFA IFFREPPKIS TKK

UniProtKB: Photosystem II reaction center protein T

+
Macromolecule #6: Photosystem II 5 kDa protein, chloroplastic

MacromoleculeName: Photosystem II 5 kDa protein, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 10.676572 KDa
SequenceString:
MASITMTASF LGTTVSKQPP THHLRRGVVM AKAMPETTTT TKEETSSKRR DLVFAVAAAA ACSVARIAMA EEPKRGTPEA KKKYAPVCV TMPSARICYK

UniProtKB: Photosystem II 5 kDa protein, chloroplastic

+
Macromolecule #7: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.186097 KDa
SequenceString:
MATITASSSA SLVARASLVH NSRVGVSSSP ILGLPSMTKR SKVTCSIENK PSTTETTTTT NKSMGASLLA AAAAATISNP AMALVDERM STEGTGLPFG LSNNLLGWIL FGVFGLIWAL YFVYASGLEE DEESGLSL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

+
Macromolecule #8: Photosystem II reaction center X protein, chloroplastic

MacromoleculeName: Photosystem II reaction center X protein, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 11.958141 KDa
SequenceString:
MASISAVSMA TPITTTTTKT TFFSPLPVVK PQRATLMGQK PRAMGLKVQA SLKEKAVTGL TAAALTASMM VPDVAEAAEL APSLKNFLF SIAAGGVVLT AIVGAVVAVS NFDPVKRA

UniProtKB: Uncharacterized protein LOC110783121

+
Macromolecule #9: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.433391 KDa
SequenceString: MASSTMALSS PSLAGKAVKL GPTASEIIGE GRITMRKTAG KPKTVQSSSP WYGPDRVKYL GPFSGEAPSY LTGEFPGDYG WDTAGLSAD PETFAKNREL EVIHCRWAML GALGCVFPEL LARNGVKFGE AVWFKAGSQI FSEGGLDYLG NPSLVHAQSI L AIWACQVI ...String:
MASSTMALSS PSLAGKAVKL GPTASEIIGE GRITMRKTAG KPKTVQSSSP WYGPDRVKYL GPFSGEAPSY LTGEFPGDYG WDTAGLSAD PETFAKNREL EVIHCRWAML GALGCVFPEL LARNGVKFGE AVWFKAGSQI FSEGGLDYLG NPSLVHAQSI L AIWACQVI LMGAVEGYRI AGGPLGEVVD PLYPGGSFDP LGLADDPEAF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GP LENLADH LADPVNNNAW NFATNFVPGK

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #10: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 6.541715 KDa
SequenceString:
MTIAFQLAVF ALIATSSILL ISVPVVFASP DGWSSNKNIV FSGTSLWLGL VFLVGILNSL IS

UniProtKB: Photosystem II reaction center protein Z

+
Macromolecule #11: Chlorophyll a-b binding protein CP24, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein CP24, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.693525 KDa
SequenceString: MAAATSATAI VNGFTSPFLS GGKKSSQSLL FVNSKVGAGV STTSRKLVVV AAAAAPKKSW IPAVKGGGNF LDPEWLDGSL PGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMLAVLGI FVGQAWTGIP WFEAGADPGA VAPFSFGTLL GTQLLLMGWV E SKRWVDFF ...String:
MAAATSATAI VNGFTSPFLS GGKKSSQSLL FVNSKVGAGV STTSRKLVVV AAAAAPKKSW IPAVKGGGNF LDPEWLDGSL PGDFGFDPL GLGKDPAFLK WYREAELIHG RWAMLAVLGI FVGQAWTGIP WFEAGADPGA VAPFSFGTLL GTQLLLMGWV E SKRWVDFF DPDSQSVEWA TPWSRTAENF SNSTGEQGYP GGKFFDPLSL AGTISNGVYN PDTDKLERLK LAEIKHARLA ML AMLIFYF EAGQGKTPLG AL

UniProtKB: Chlorophyll a-b binding protein CP24, chloroplastic

+
Macromolecule #12: Oxygen-evolving enhancer protein 2, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 2, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.495918 KDa
SequenceString: MASTACFLHH HAAISSPAAG RGSAAQRYQA VSIKPNQIVC KAQKQDDNEA NVLNSGVSRR LALTVLIGAA AVGSKVSPAD AAYGEAANV FGKPKKNTEF MPYNGDGFKL LVPSKWNPSK EKEFPGQVLR YEDNFDATSN LSVLVQPTDK KSITDFGSPE D FLSQVDYL ...String:
MASTACFLHH HAAISSPAAG RGSAAQRYQA VSIKPNQIVC KAQKQDDNEA NVLNSGVSRR LALTVLIGAA AVGSKVSPAD AAYGEAANV FGKPKKNTEF MPYNGDGFKL LVPSKWNPSK EKEFPGQVLR YEDNFDATSN LSVLVQPTDK KSITDFGSPE D FLSQVDYL LGKQAYFGKT DSEGGFDSGV VASANVLESS TPVVDGKQYY SITVLTRTAD GDEGGKHQVI AATVKDGKLY IC KAQAGDK RWFKGAKKFV ESATSSFSVA

UniProtKB: Oxygen-evolving enhancer protein 2, chloroplastic

+
Macromolecule #13: Oxygen-evolving enhancer protein 3, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 3, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.884426 KDa
SequenceString: MAQAMASMAG LRGASQAVLE GSLQISGSNR LSGPTTSRVA VPKMGLNIRA QQVSAEAETS RRAMLGFVAA GLASGSFVKA VLAEARPIV VGPPPPLSGG LPGTENSDQA RDGTLPYTKD RFYLQPLPPT EAAQRAKVSA SEILNVKQFI DRKAWPSLQN D LRLRASYL ...String:
MAQAMASMAG LRGASQAVLE GSLQISGSNR LSGPTTSRVA VPKMGLNIRA QQVSAEAETS RRAMLGFVAA GLASGSFVKA VLAEARPIV VGPPPPLSGG LPGTENSDQA RDGTLPYTKD RFYLQPLPPT EAAQRAKVSA SEILNVKQFI DRKAWPSLQN D LRLRASYL RYDLKTVISA KPKDEKKSLQ ELTSKLFSSI DNLDHAAKIK SPTEAEKYYG QTVSNINEVL AKLG

UniProtKB: Oxygen-evolving enhancer protein 3, chloroplastic

+
Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.429234 KDa
SequenceString: MASSTMALSS PAFGGKAVKL NPSTSDMIGE GRISMRKSAG KPKNVSSGSP WYGPDRVKYL GPFSGEAPSY LTGEFPGDYG WDTAGLSAD PETFSKNREL EVIHCRWAML GALGCVFPEL LARNGVKFGE AVWFKAGSQI FSEGGLDYLG NPSLVHAQSI L AIWACQVI ...String:
MASSTMALSS PAFGGKAVKL NPSTSDMIGE GRISMRKSAG KPKNVSSGSP WYGPDRVKYL GPFSGEAPSY LTGEFPGDYG WDTAGLSAD PETFSKNREL EVIHCRWAML GALGCVFPEL LARNGVKFGE AVWFKAGSQI FSEGGLDYLG NPSLVHAQSI L AIWACQVI LMGAVEGYRV AGGPLGEVVD PLYPGGSFDP LGLAEDPEAF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GP LENLADH LADPVNNNAW NFATNFVPGN

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Details: NCBI Reference Sequence: XP_021861951.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 28.512396 KDa
SequenceString: MATMVSSSTV LTPNPFVGQG KGANGNTLRD VVPMGSGKFT MGNDLWYGPD RVKYLGPFSA QTPSYLTGEF PGDYGWDTAG LSADPEAFA RNRALEVIHG RWAMLGALGC LTPEVLEKWV KVDFKEPVWF KAGAQIFSEG GLDYLGNPNL VHAQSILAVL G FQVLLMGL ...String:
MATMVSSSTV LTPNPFVGQG KGANGNTLRD VVPMGSGKFT MGNDLWYGPD RVKYLGPFSA QTPSYLTGEF PGDYGWDTAG LSADPEAFA RNRALEVIHG RWAMLGALGC LTPEVLEKWV KVDFKEPVWF KAGAQIFSEG GLDYLGNPNL VHAQSILAVL G FQVLLMGL VESFRINGLD GVGDGNDLYP GGQYFDPLGL ADDPVTFAEL KVKEIKNGRL AMFSMFGFFV QAIITGKGPL EN LLDHLDN PVANNAWVYA TKFVPGS

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #16: Photosystem II 10 kDa polypeptide, chloroplastic

MacromoleculeName: Photosystem II 10 kDa polypeptide, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 14.409401 KDa
SequenceString:
MATSVMSSLS LKPSSFGVDT KSAVKGLPSL SRSSASFTVR ASGVKKIKVD KPLGIGGGMK LRDGVDSSGR KPTGKGVYQF VDKYGANVD GYSPIYNEEE WAPTGDVYAG GTTGLLIWAV TLAGLLAGGA LLVYNTSALA Q

UniProtKB: Photosystem II 10 kDa polypeptide, chloroplastic

+
Macromolecule #17: Photosystem II reaction center proteins PsbY, chloroplastic

MacromoleculeName: Photosystem II reaction center proteins PsbY, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 20.678209 KDa
SequenceString: MAATMATTMA VLNTKCLTLN TNKTTSTSPK PTSKPISLSP LGLSNSKLPM GLSPIITAPA IAGAVFATLG SVDPAFAVQQ LADIAAEAG TSDNRGLALL LPIIPALGWV LFNILQPALN QINKMRNEKK AFIVGLGLSG LATSGLLLAT PEAQAASEEI A RGSDNRGT ...String:
MAATMATTMA VLNTKCLTLN TNKTTSTSPK PTSKPISLSP LGLSNSKLPM GLSPIITAPA IAGAVFATLG SVDPAFAVQQ LADIAAEAG TSDNRGLALL LPIIPALGWV LFNILQPALN QINKMRNEKK AFIVGLGLSG LATSGLLLAT PEAQAASEEI A RGSDNRGT LLLLVVLPAI GWVLFNILQP ALNQLNKMRS Q

UniProtKB: Photosystem II reaction center proteins PsbY, chloroplastic

+
Macromolecule #18: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 51.880559 KDa
SequenceString: MKTLYSLRRF YPVETLFNGT LTLAGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL ...String:
MKTLYSLRRF YPVETLFNGT LTLAGRDQET TGFAWWAGNA RLINLSGKLL GAHVAHAGLI VFWAGAMNLF EVAHFVPEKP MYEQGLILL PHLATLGWGV GPGGEVIDTF PYFVSGVLHL ISSAVLGFGG IYHALLGPET LEESFPFFGY VWKDRNKMTT I LGIHLILL GIGAFLLVFK ALYFGGVYDT WAPGGGDVRK ITNVTLSPSI IFGCLLKSPF GGEGWIVSVD DLEDIIGGHV WI GVICILG GIWHILTKPF AWARRALVWS GEAYLSYSLA ALSVFGFIAC 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 #19: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 19 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 39.422016 KDa
SequenceString: MTIAVGKFTK DEKDLFDSMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHS LLLLWGPEAQ GDFTRWCQLG GLWAFVALHG AFALIGFMLR QFELARSVQL RPYNAIAFSG PIAVFVSVFL I YPLGQSGW ...String:
MTIAVGKFTK DEKDLFDSMD 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 LPRGNA

UniProtKB: Photosystem II D2 protein

+
Macromolecule #20: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 20 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 9.393501 KDa
SequenceString:
MSGSTGERSF ADIITSIRYW VIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTESR QGIPLITGRF DSLEQLDEFS RSF

UniProtKB: Cytochrome b559 subunit alpha

+
Macromolecule #21: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 21 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 4.502351 KDa
SequenceString:
MTIDRTYPIF TVRWLAIHGL AVPTVFFLGS ISAMQFIQR

UniProtKB: Cytochrome b559 subunit beta

+
Macromolecule #22: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 22 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 7.735004 KDa
SequenceString:
MATQTVESSS RSRPKPTTVG ALLKPLNSEY GKVAPGWGTT PLMGVAMALF AVFLSIILEI YNSSVLLDGI SMN

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #23: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 4.170891 KDa
SequenceString:
MLTLKLFVYT VVIFFVSLFI FGFLSNDPGR NPGREE

UniProtKB: Photosystem II reaction center protein I

+
Macromolecule #24: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 24 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 4.117832 KDa
SequenceString:
MADTTGRIPL WIIGTVAGIL VIGLVGIFFY GSYSGLGSSL

UniProtKB: Photosystem II reaction center protein J

+
Macromolecule #25: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 25 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 6.751023 KDa
SequenceString:
MLNIFSLICL NSALYSSSFF FGKLPEAYAF LSPIVDFMPV IPLFFFLLAF VWQAAVSFR

UniProtKB: Photosystem II reaction center protein K

+
Macromolecule #26: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 26 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 4.4981 KDa
SequenceString:
MTQSNPNEQN VELNRTSLYW GLLLIFVLAV LFSNYFFN

UniProtKB: Photosystem II reaction center protein L

+
Macromolecule #27: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 27 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 3.783538 KDa
SequenceString:
MEVNILAFIA TALFILVPTA FLLIIYVKTV SQND

UniProtKB: Photosystem II reaction center protein M

+
Macromolecule #28: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 28 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 56.207852 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLI SVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWSI TGGTITDPG IWSYEGVAGA HIMFSGLCFL AAIWHWVYWD LEIFSDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLI SVHIMHTALV AGWAGSMALY ELAVFDPSDP VLDPMWRQGM FVIPFMTRLG ITNSWGGWSI TGGTITDPG IWSYEGVAGA HIMFSGLCFL AAIWHWVYWD LEIFSDERTG KPSLDLPKIF GIHLFLSGVA CFGFGAFHVT G LYGPGIWV SDPYGLTGKV QPVSPAWGVE GFDPFVPGGI ASHHIAAGTL GILAGLFHLS VRPPQRLYKG LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSATTPIEL FGPTRYQWDQ GYFQQEIYRR VSAGLAENQS FSEAWSKIPE KLAFYDYIGN NPA KGGLFR AGSMDNGDGI AVGWLGHPIF RDKEGRELFV RRMPTFFETF PVVLIDGDGI VRADVPFRRA ESKYSVEQVG VTVE FYGGE LNGVSYSDPA TVKKYARRAQ LGEIFELDRA TLKSDGVFRS SPRGWFTFGH ASFALLFFFG HIWHGSRTLF RDVFA GIDP DLDVQVEFGA FQKIGDPTTR RQGV

UniProtKB: Photosystem II CP47 reaction center protein

+
Macromolecule #29: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 29 / Number of copies: 4 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #30: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 30 / Number of copies: 4 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #31: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 31 / Number of copies: 8 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #32: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 32 / Number of copies: 374 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #33: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 33 / Number of copies: 8 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #34: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 34 / Number of copies: 44 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #35: 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: 35 / Number of copies: 6 / 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 #36: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 36 / Number of copies: 55 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #37: 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: 37 / Number of copies: 14 / 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 #38: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 38 / Number of copies: 22 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #39: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 39 / Number of copies: 140 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #40: (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: 40 / Number of copies: 38 / 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 #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: 18 / 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: (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: 42 / Number of copies: 14 / 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 #43: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 43 / Number of copies: 4 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

+
Macromolecule #44: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 44 / Number of copies: 20 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #45: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 45 / Number of copies: 4 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

+
Macromolecule #46: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 46 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3jcu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93684
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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