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- EMDB-33929: PSII-Pcb Dimer of Acaryochloris Marina -

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Basic information

Entry
Database: EMDB / ID: EMD-33929
TitlePSII-Pcb Dimer of Acaryochloris Marina
Map data
Sample
  • Complex: PSII-Pcb Dimer of Acaryochloris Marina
    • Protein or peptide: x 20 types
  • Ligand: x 12 types
KeywordsPhotosystem II / Pcb / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem / 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 / response to herbicide / photosystem II / photosynthesis, light reaction ...photosystem / 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 / response to herbicide / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbY / Photosystem II PsbX, type 1 subfamily / 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 PsbY / Photosystem II PsbX, type 1 subfamily / 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 CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / 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 / Photosystem II protein D1 / 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 protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein 1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Y / High light inducible protein / High light inducible protein / High light inducible protein / Photosystem II protein PsbI ...Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein 1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Y / High light inducible protein / High light inducible protein / High light inducible protein / Photosystem II protein PsbI / Photosystem II protein PsbT / High light inducible protein / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Photosystem II reaction center protein K / Photosystem II 10 kDa phosphoprotein PsbH / Photosystem II reaction center protein M / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShen LL / Gao YZ / Wang WD / Zhang X / Shen JR / Wang PY / Han GY
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Chinese Academy of SciencesXDB17000000 China
National Basic Research Program of China (973 Program)2015CB150100 China
CitationJournal: Sci Adv / Year: 2024
Title: Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll -containing cyanobacterium.
Authors: Liangliang Shen / Yuanzhu Gao / Kailu Tang / Ruxi Qi / Lutang Fu / Jing-Hua Chen / Wenda Wang / Xiaomin Ma / Peiyao Li / Min Chen / Tingyun Kuang / Xing Zhang / Jian-Ren Shen / Peiyi Wang / Guangye Han /
Abstract: is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl- ... is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.
History
DepositionJul 28, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33929.png

Downloads & links

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Map

FileDownload / File: emd_33929.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0188
Minimum - Maximum-0.040508855 - 0.08321751
Average (Standard dev.)0.00012799191 (±0.0016386111)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 513.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33929_msk_1.map
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Half map: #1

Fileemd_33929_half_map_1.map
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Half map: #2

Fileemd_33929_half_map_2.map
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Sample components

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Entire : PSII-Pcb Dimer of Acaryochloris Marina

EntireName: PSII-Pcb Dimer of Acaryochloris Marina
Components
  • Complex: PSII-Pcb Dimer of Acaryochloris Marina
    • Protein or peptide: Photosystem II protein D1 2
    • 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 1
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Photosystem II protein Y
    • Protein or peptide: Photosystem II 10 kDa phosphoprotein PsbH
    • Protein or peptide: Photosystem II protein PsbI
    • 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: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: High light inducible protein
    • Protein or peptide: Unknown protein
    • Protein or peptide: High light inducible protein
    • Protein or peptide: High light inducible protein
    • Protein or peptide: High light inducible protein
  • Ligand: CHLOROPHYLL D
  • Ligand: PHEOPHYTIN A
  • Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: FE (II) ION
  • Ligand: BICARBONATE ION
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

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Supramolecule #1: PSII-Pcb Dimer of Acaryochloris Marina

SupramoleculeName: PSII-Pcb Dimer of Acaryochloris Marina / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)

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Macromolecule #1: Photosystem II protein D1 2

MacromoleculeName: Photosystem II protein D1 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 39.695211 KDa
SequenceString: MTTVLQRRES ASAWERFCSF ITSTNNRLYI GWFGVLMIPT LLTAVTCFVI AFIGAPPVDI DGIREPVAGS LLYGNNIITG AVVPSSNAI GLHLYPIWEA ASLDEWLYNG GPYQLIIFHY MIGCICYLGR QWEYSYRLGM RPWICVAYSA PLAATYSVFL I YPLGQGSF ...String:
MTTVLQRRES ASAWERFCSF ITSTNNRLYI GWFGVLMIPT LLTAVTCFVI AFIGAPPVDI DGIREPVAGS LLYGNNIITG AVVPSSNAI GLHLYPIWEA ASLDEWLYNG GPYQLIIFHY MIGCICYLGR QWEYSYRLGM RPWICVAYSA PLAATYSVFL I YPLGQGSF SDGMPLGISG TFNFMFVFQA EHNILMHPFH MFGVAGVLGG SLFAAMHGSL VSSTLVRETT EGESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFSN SRSLHFFLGA WPVVCIWLTA MGISTMAFNL NGFNFNHSIV DSQGNVVNTW ADV LNRANL GFEVMHERNA HNFPLDLAAG ESAPVALTAP VING

UniProtKB: Photosystem II protein D1 2

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 56.518746 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLL SVHLMHTALV SGWAGSMALY ELAKYDPSDP VLNPMWRQGT FVMPVMTRIG VTHSWSGWTV TGEPWVTQP GILGAHLNFF SYEGVILMHI LAAGLFFLAA VWHWINWDLD IYYPDGSSEP ASDWPKIFGL HLLTLGIVCF G FGSLHLTG ...String:
MGLPWYRVHT VVLNDPGRLL SVHLMHTALV SGWAGSMALY ELAKYDPSDP VLNPMWRQGT FVMPVMTRIG VTHSWSGWTV TGEPWVTQP GILGAHLNFF SYEGVILMHI LAAGLFFLAA VWHWINWDLD IYYPDGSSEP ASDWPKIFGL HLLTLGIVCF G FGSLHLTG ILGPGMWVSD PYGLTGHVQG VSPDWRPFAF DPYNPTGLVT HHISAGIALI IGGIFHTVSR PSERLYNALS MG NVETVLS SSVAFVAAAA FVMVGTMWYG SATTPIELFG PTRYQWDSGY FQTEIQRRVQ SGQTWDQIPE KLVFYDYIGN SPA KGGLFR TGAMNSGDGI ARAWEGHPTF TDSEGRELFV RRMPNFFETF PVVLTDKDGV VRADIPFRRA ESRYSFEQKG VSVS FEGGT LNGQTFTDAP SVKKYARKAQ LGEPFEFDRE TLGSDGVFRT STRGWFAFSH SCYALLFFFG HWWHGARTIF KDVFE GVDP NLPEEQVEWG VFQKVGDTTT RA

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 53.97832 KDa
SequenceString: MKVCALGWHP KTKSMKTSSS LRRFYHVETP FNPSAAGYDR ATTGYGWWAG NARLTDLSGQ LTGAHIAHAG MITFWAGAMT LFEVSHFIP EKPMYEQGSI LLAHLAAEGF GVGPGGEVIS TYPYFVIGAI HLIASAVLGF GGLYHTFRGP AKFEDYSDWW G YDWEDKEK ...String:
MKVCALGWHP KTKSMKTSSS LRRFYHVETP FNPSAAGYDR ATTGYGWWAG NARLTDLSGQ LTGAHIAHAG MITFWAGAMT LFEVSHFIP EKPMYEQGSI LLAHLAAEGF GVGPGGEVIS TYPYFVIGAI HLIASAVLGF GGLYHTFRGP AKFEDYSDWW G YDWEDKEK MMQILGIHLI FLGIGALAFA AKAMFFGGLY DPWAPGGGNV RLITNPTWNL GTFLGYITRS PWGEGGWIVS VN NLEDVVG GHLLVGVHYI FGGVFHILVK PWGWVRRAYV WSGEAYLSYS LGALYMCGMI AVGYVWFNNT VYPSEFYGPT AAE ASQAQA MTFLIRDQRL GANIASAQGP TGLGKYLMRS PSGEIIFGGE TMRFWDFRGP WLEPLRGPNG LDLNKLRNDI QPWQ ARRAA EYMTHAPLGA LNSVGGVATE INSVNYVSPR SWLSTSHFCL AFFFFVGHIW HSGRARAAAA GFEKGIERKT EYALS LPDI DATSVD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #4: Photosystem II D2 protein 1

MacromoleculeName: Photosystem II D2 protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 39.291852 KDa
SequenceString: MTIAVGRAQE RGWFDVLDDW LKRDRFVFIG WSGILLFPCA FLSIGGWFTG TTFVTSWYTH GLASSYLEGA NFLTVAVSTP ADSLGHSLL LLWGPEAQGD FTRWCQLGGL WNFTTLHGVF GLIGFMLRQF EIARLVGVRP YNAVAFSGPI AVYVSVFLMY P LGQSSWFF ...String:
MTIAVGRAQE RGWFDVLDDW LKRDRFVFIG WSGILLFPCA FLSIGGWFTG TTFVTSWYTH GLASSYLEGA NFLTVAVSTP ADSLGHSLL LLWGPEAQGD FTRWCQLGGL WNFTTLHGVF GLIGFMLRQF EIARLVGVRP YNAVAFSGPI AVYVSVFLMY P LGQSSWFF APSWGVTSIF RFLLFAQGFH NLTLNPFHMM GVAGILGGAL LCAIHGATVE NTLFEDGQDA NTFAAFTPTQ AE ETYSMVT ANRFWSQIFG IAFSNKRWLH FFMLFVPVTG LWASAIGLVG IALNMRAYDF VSQEIRAAED PEFETFYTKN ILL NEGLRA WMAPQDQIHE NFIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein 1

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 9.495788 KDa
SequenceString:
MSGRTGERPF GDIVTSIRYW IIHTITVPML FLAGWLFVST GLAYDVFGTP RPNEYFDQAR QGLPLVTDRY EGKQQIDEFT KGL

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Photosystem II protein Y

MacromoleculeName: Photosystem II protein Y / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 11.27732 KDa
SequenceString:
MTARTQLQRP PQRKYPIYTV RWLAVHTLGV PLVWFLGAIA SMQFINRMDA YEAVAPTMIA GIDLRLALVL APILFSVVWN VIFFGGPTL QELQEVLQRE

UniProtKB: Photosystem II reaction center protein Y

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Macromolecule #7: Photosystem II 10 kDa phosphoprotein PsbH

MacromoleculeName: Photosystem II 10 kDa phosphoprotein PsbH / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 7.683901 KDa
SequenceString:
MPKQTWWGDV LKGNNNSEAG KFVPGWGTTP VMAGFVVMIT LLLLIMLQVY NHTIVLDGVD AGWTSLGGFG Q

UniProtKB: Photosystem II 10 kDa phosphoprotein PsbH

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Macromolecule #8: Photosystem II protein PsbI

MacromoleculeName: Photosystem II protein PsbI / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 3.948692 KDa
SequenceString:
MAILKFVTYA WIIFVISLFF FGFISSDTTR NPKA

UniProtKB: Photosystem II protein PsbI

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Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 4.939008 KDa
SequenceString:
MEAVLLLAKL PEAFSVFSPI VDVMPVIPLF FLALAFVWQA AVGFK

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 4.254045 KDa
SequenceString:
MATPNPNKQP VELNRASLFI GLLLVLVLAL LFSSYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #11: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 3.614302 KDa
SequenceString:
MPVNDLGAIA TALFVFIPCV FLILLYAQTA SRGS

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 5.442383 KDa
SequenceString:
MDVIAYVFIL ACIIGLFFFA VFFREKPTLD KIQSRSFRES SQSTRR

UniProtKB: Photosystem II protein PsbT

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Macromolecule #13: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 4.443303 KDa
SequenceString:
MTITPSLQGF FYSILFGAIV LGLLGGGFIF FSQKDKIVRR

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #14: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 4.015932 KDa
SequenceString:
MDLLAAINLQ VVLQLTMLGA VVIAGPIVVL LVALRSNAT

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Macromolecule #15: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 6.395632 KDa
SequenceString:
MSVLFQLLIA AFVALSFAMI IGVPVVFSTG DASDDANKLI WGGAAAWVVL LFVAALASIV VI

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #16: High light inducible protein

MacromoleculeName: High light inducible protein / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 38.753934 KDa
SequenceString: MQTYGNQNVE YGWWSGNSRF TDFSAQFLAA HIGQIASMTF FAGSITLFEL SRYNPDIPLY AQGFVCLPQL SRVGFGVGAG GAVVDTYPF FAVGMIHLFA AAVFGSGAIF HILTGPKVLA DSDSAASQRF HFEWDDFETQ GRILGHHLLF LGSGALLFVV W AATHGIYD ...String:
MQTYGNQNVE YGWWSGNSRF TDFSAQFLAA HIGQIASMTF FAGSITLFEL SRYNPDIPLY AQGFVCLPQL SRVGFGVGAG GAVVDTYPF FAVGMIHLFA AAVFGSGAIF HILTGPKVLA DSDSAASQRF HFEWDDFETQ GRILGHHLLF LGSGALLFVV W AATHGIYD PNVGEVRAVS PGFDIVRIFK YGWATPGFNP FFVDNLEDVM GGHLFIALID IAGGIYHILV KPWPYTERIF TK SGEALLG YALGGLGLMG LVAAYFCSVN DVVFPVEFFG PVLQPNLGFL PNFADTLDVS ASGHTSRFWI ANFHYFWGFY CIQ GHLFHA LRASGFDFRV LTKFFTTETV ELGADI

UniProtKB: High light inducible protein

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Macromolecule #17: Unknown protein

MacromoleculeName: Unknown protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 3.507314 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #18: High light inducible protein

MacromoleculeName: High light inducible protein / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 38.612156 KDa
SequenceString: MATKVDTAPE YPWYSGNSRL EDPAVQGKWL AAHIAQIALI VFWVGLNTFS ENQAFDTSLP MFDQGLVLIP HLAALGFGVG SGGVVTNTF VFTQIGAIHM VSSFVLFGGA YFHAKIGPSV LADGGRGNTD QFAFSWDDPK KLGYILGHHL VLIGTGALLF V LWIKFHGI ...String:
MATKVDTAPE YPWYSGNSRL EDPAVQGKWL AAHIAQIALI VFWVGLNTFS ENQAFDTSLP MFDQGLVLIP HLAALGFGVG SGGVVTNTF VFTQIGAIHM VSSFVLFGGA YFHAKIGPSV LADGGRGNTD QFAFSWDDPK KLGYILGHHL VLIGTGALLF V LWIKFHGI YDPTIGEVRT VAAPGSTIGD VVLKYGWFTP GYNCFFVDNL EDLASGHLFI GLVDIAGGIF HINVAPLPWS KV VNKYTYS PDGLLGTAIG GLALMGFISA YFCAVNTLVY PVEFFGPALE VKFGIAPYFK DTADLADGFY TSRAWLANIT YYL AFYMLQ GHLYHTLKAM GFKFEDIPAV IARDTGNAPA

UniProtKB: High light inducible protein

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Macromolecule #19: High light inducible protein

MacromoleculeName: High light inducible protein / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 38.707781 KDa
SequenceString: MQTYGQTDVE YGWWSGNSRF SDYSGQFLAA HNGQIASMCF WAGSFTLFEV SRFNPDLPVY QQNLVCIPQL ARAGWGVAAG GAVVDTYPY FAIAMIHLVA AAILGAGALY GVTKGPKVLA DSEFSGAQRF HFEWDDFETQ GRILGHHLLF LGAACLLFAT W ACTHGVYD ...String:
MQTYGQTDVE YGWWSGNSRF SDYSGQFLAA HNGQIASMCF WAGSFTLFEV SRFNPDLPVY QQNLVCIPQL ARAGWGVAAG GAVVDTYPY FAIAMIHLVA AAILGAGALY GVTKGPKVLA DSEFSGAQRF HFEWDDFETQ GRILGHHLLF LGAACLLFAT W ACTHGVYD PVAGEVRAIS PSLNLVRFFK YGWATPGFNP YFVNNLEDVI GGHFFVSSLY IAGGIWHILV KPWPYTDKIF VK SGEALLA YALAGLAFAG FNAAYFCSVN DVVFPVELFG PVLEAKLNVT PYFAETLDAS DGGHTTRFWI SNFHYYWAFY CLQ GHLFHA LRSYGFDFRR IPRALASLTP QAN

UniProtKB: High light inducible protein

+
Macromolecule #20: High light inducible protein

MacromoleculeName: High light inducible protein / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
Molecular weightTheoretical: 37.967473 KDa
SequenceString: MTASVRGRRG GKVAVQTDLP TSVLSNFENE WWAGNVRMTD LSGMLLGAHL CHAALMSVVP GAFIVQEVAR YQPGVSLPDQ GMIFMPHLA ALGVGVGAGG EIVDTYPFFV IGVLHFFIAA VCCAAGLFHT FRGETDLNDA PDDSYAAAFR YEWDDFESLS T IVGHHLVF ...String:
MTASVRGRRG GKVAVQTDLP TSVLSNFENE WWAGNVRMTD LSGMLLGAHL CHAALMSVVP GAFIVQEVAR YQPGVSLPDQ GMIFMPHLA ALGVGVGAGG EIVDTYPFFV IGVLHFFIAA VCCAAGLFHT FRGETDLNDA PDDSYAAAFR YEWDDFESLS T IVGHHLVF ISVACLIFAV NATYGTGMYD INTDTVHQIS PNLNPITLIG YLFGFTPDGW SGAGMAAVNN MEDVIGGHFL IG VIDLLGA AFHILYRKPT PLFTKHPVFS PANGGWSNVG MLNSELILSW SVASVGFMGI SSSLFIRYCD VAYPPVFHGV DRT GAATLQ LILGLVWMLG GGLWHGLRGE RLYAANK

UniProtKB: High light inducible protein

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Macromolecule #21: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 21 / Number of copies: 212 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

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Macromolecule #22: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 22 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #23: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

MacromoleculeName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
type: ligand / ID: 23 / Number of copies: 22 / Formula: 8CT
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-8CT:
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene

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Macromolecule #24: 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: 24 / 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

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Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 25 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 26 / Number of copies: 8 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / 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 #28: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 28 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #29: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 29 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Macromolecule #30: 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: 30 / 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 #31: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 31 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #32: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...

MacromoleculeName: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
type: ligand / ID: 32 / Number of copies: 28 / Formula: ZEX
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-ZEX:
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132346
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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