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- EMDB-37749: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis -

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Basic information

Entry
Database: EMDB / ID: EMD-37749
TitleIn situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis
Map data
Sample
  • Cell: In situ PBS-PSII supercomplex
    • Protein or peptide: x 32 types
  • Ligand: x 16 types
Keywordscomplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
: / : / : / : / : / : / : / : / : / : ...: / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / Phycocyanin beta subunit
Similarity search - Component
Biological speciesArthrospira platensis (bacteria) / Arthrospira sp. FACHB-439 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYou X / Zhang X / Xiao YN / Sun S / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: In situ structural determination of cyanobacterial phycobilisome-PSII supercomplex by STAgSPA strategy.
Authors: Xing Zhang / Yanan Xiao / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) ...Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) and transferred to photosynthetic reaction centers of photosystem II (PSII) and photosystem I (PSI). While most of the protein complexes involved in photosynthesis have been characterized by in vitro structural analyses, how these protein complexes function together in vivo is not well understood. Here we implemented STAgSPA, an in situ structural analysis strategy, to solve the native structure of PBS-PSII supercomplex from the cyanobacteria Arthrospira sp. FACHB439 at resolution of ~3.5 Å. The structure reveals coupling details among adjacent PBSs and PSII dimers, and the collaborative energy transfer mechanism mediated by multiple super-PBS in cyanobacteria. Our results provide insights into the diversity of photosynthesis-related systems between prokaryotic cyanobacteria and eukaryotic red algae but are also a methodological demonstration for high-resolution structural analysis in cellular or tissue samples.
History
DepositionOct 11, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37749.png

Downloads & links

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Map

FileDownload / File: emd_37749.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 400 pix.
= 652.8 Å		1.63 Å/pix.
x 400 pix.
= 652.8 Å		1.63 Å/pix.
x 400 pix.
= 652.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.2083731 - 1.7229733
Average (Standard dev.)0.0061444305 (±0.05728168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : In situ PBS-PSII supercomplex

EntireName: In situ PBS-PSII supercomplex
Components
  • Cell: In situ PBS-PSII supercomplex
    • Protein or peptide: LRC1
    • Protein or peptide: LCM
    • Protein or peptide: Allophycocyanin alpha chain
    • Protein or peptide: Allophycocyanin beta chain
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • 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: Photosystem II extrinsic protein O
    • Protein or peptide: PsbQ protein
    • Protein or peptide: Photosystem II reaction center protein Y
    • Protein or peptide: LPP1
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: PsbU
    • Protein or peptide: Photosystem II extrinsic protein V
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: LPP2
    • Protein or peptide: Allophycocyanin beta-18 subunit
    • Protein or peptide: Allophycocyanin-B alpha subunit
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: Phycocyanin beta subunit
  • Ligand: PHYCOCYANOBILIN
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • 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-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PHEOPHYTIN A
  • Ligand: FE (II) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION

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Supramolecule #1: In situ PBS-PSII supercomplex

SupramoleculeName: In situ PBS-PSII supercomplex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Arthrospira platensis (bacteria)

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Macromolecule #1: LRC1

MacromoleculeName: LRC1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 29.443213 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MVPLPLLSYT TTSFNTRVAG YEVPGDEQPQ IYTAENMPSG SEWDTLIWAA YRQIFSEHQM LKSNRQTFLE SQLKFGQITV RDFIGGLAT SAPFLERNYQ TNSNYRFAEM CVQRILGRDV YNEREKIAWS IVIANKGPKG FIEELLNSDE YLDNFGYDTV P YQRRRVLP ...String:
MVPLPLLSYT TTSFNTRVAG YEVPGDEQPQ IYTAENMPSG SEWDTLIWAA YRQIFSEHQM LKSNRQTFLE SQLKFGQITV RDFIGGLAT SAPFLERNYQ TNSNYRFAEM CVQRILGRDV YNEREKIAWS IVIANKGPKG FIEELLNSDE YLDNFGYDTV P YQRRRVLP QRNVGETPFN LKTPRYNEYH RTQLGFPQVI WQTSVRRFVP QEKQPKAGDP ANFLAMAKQV SRPANTVTRV AL GSINFDT MVPYRQR

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Macromolecule #2: LCM

MacromoleculeName: LCM / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 102.100633 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MSVKASGGSS VARPQLYKTV PVSTISQAEQ QDRYLGKTEL SDLATYFSSG AKRLEIAQVL TQNAELIVSR AANRIFTGGS PLAFLERPE EPEMAMAAAG SGDMEVAEGM KLGTISYVDN RGGGFFDGIK SLFQDSGTGP AVFLPPGFRP INVSRYGPGN M TKSLRDLS ...String:
MSVKASGGSS VARPQLYKTV PVSTISQAEQ QDRYLGKTEL SDLATYFSSG AKRLEIAQVL TQNAELIVSR AANRIFTGGS PLAFLERPE EPEMAMAAAG SGDMEVAEGM KLGTISYVDN RGGGFFDGIK SLFQDSGTGP AVFLPPGFRP INVSRYGPGN M TKSLRDLS WFLRYTTYAI VAGDPNIIAV NVRGLREIIE NACSSAATLV ALQEMRRSAL GYLQNDKEGQ EIALQYFNVL IS EFEGATP SNKVRQGQSV DQQGLELPQI YFNAAEARQK FVMKSGMSSS EKLDVVKAAY RQVFERDITR AYSQGISDLE SKF KNGEIS TKEFIRRLGK SPLYRQQFYS RFVNSRVVEL AARHFLGRGL SSPEEFSKYF AIVTKGGLAA LVDAMVDSTE YADY FGEET VPYLRGLGTE AQECRNWGPQ IDLFNYSAPF RKVPQFVTLF GDYKQPLRDQ HVYGIGNDPL EIQFGAIFPK ETRSP KNRP APFGKDTRRI LIHNGAGIDN QLSNPGARGN APGSLGPKVF KLDQLPGGYI SSKFSNKGGN SGASVKFSES STQKVI RAA YLQVFGRELY SGQRQTVAEI KLENGDITVR EFIRILAKSD VFRNMYWTSL YVCKAIEYIH RRLLGRPTYG RQEMNSY FD LCSKKGFYAL VDAIIDSVEY NEAFGEDTIP YERYLTPGGL SLRSMRVGTL AEKMTMVKDE PTPRFVELGT PTDQMKGE L EIDNQIKQGV NKRREQSKVF KLTNVTDKVA LQTTIGAIYR QIFERDIDPY VTKKEFTALE SKLGNGEITV KEFVEALGA SALYIREFYT PYPNTKVIEL GTKHFLGRAP LNQAEIRKYN QILASQGLKA FIGAMVNSME YAQVFGEDTV PYRRFPTLPA ANFPNTELL YNQLTKQNDE LVVPSFEPVL ANDRS

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Macromolecule #3: Allophycocyanin alpha chain

MacromoleculeName: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 17.409799 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MSIVTKSIVN ADAEARYLSP GELDRIKSFV TSGERRVRIA ETMTGARERI IKEAGNQLFQ KRPDVVSPGG NAYGEEMTAT CLRDLDYYL RLITYGIVAG DVTPIEEIGV VGVREMYKSL GTPIEAVAEG VRAMKSVATS LLSGEDAAEA GAYFDYLIGA M S

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Macromolecule #4: Allophycocyanin beta chain

MacromoleculeName: Allophycocyanin beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 68 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 17.345748 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MQDAITSVIN SSDVQGKYLD ASAIQKLKAY FATGELRVRA ATTISANAAN IVKEAVAKSL LYSDITRPGG NMYTTRRYAA CIRDLDYYL RYATYAMLAG DPSILDERVL NGLKETYNSL GVPIGATVQA IQAMKEVTAG LVGADAGKEM GIYFDYICSG L S

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Macromolecule #5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 7.775107 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MRSFKVTACV PSQTRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVELATGKP GTNTGLL

UniProtKB: UNIPROTKB: A0A9W3ZBQ2

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Macromolecule #6: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 39.675184 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MTTTLQQREN LNIWEQFCGW VTSTNNRLYV GWFGIVMIPT LLTATICFVL AFVAAPPVDI DGIREPVSGS LLYGNNIITA AVVPSSNAI GLHFYPIWEA ANIDEWLYNG GPYQLIVFHF LIGIFCYMGR EWELSYRLGM RPWIAVAYSA PVAAATAVLL V YSIGQGSF ...String:
MTTTLQQREN LNIWEQFCGW VTSTNNRLYV GWFGIVMIPT LLTATICFVL AFVAAPPVDI DGIREPVSGS LLYGNNIITA AVVPSSNAI GLHFYPIWEA ANIDEWLYNG GPYQLIVFHF LIGIFCYMGR EWELSYRLGM RPWIAVAYSA PVAAATAVLL V YSIGQGSF SDGLPLGISG TFNFMLVLQA EHNVLMHPFH MLGVAGVFGG ALFSAMHGSL VTSSLVRETT EIESQNRGYR FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLGA WPVVGIWFAS LAVACFAFNL NGFNFNHSVL DSQGKVLNTW ADV INRANL GIEAMHERNV HNFPLDLAST ESKPVNLVAP NIG

UniProtKB: UNIPROTKB: A0A9W4ENJ6

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Macromolecule #7: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 56.256766 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARLG VTQSWGGWSL TGEVADNPG IWSFEGVAAT HIILSGLLFL AAVWHWVYWD LELFTDPRTG EPALDLPKMF GIHLFLSGLL CFGFGAFHLT G LFGPGMWV ...String:
MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARLG VTQSWGGWSL TGEVADNPG IWSFEGVAAT HIILSGLLFL AAVWHWVYWD LELFTDPRTG EPALDLPKMF GIHLFLSGLL CFGFGAFHLT G LFGPGMWV SDPYGLTGSI QPVAPSWGPE GFNPFNAGGI AAHHIAAGIV GIIAGLFHLS VRPPQRLYKA LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSAATPIEL FGPTRYQWDQ GYFQQEIQRR VQSSIAQGDS PSEAWSKIPE KLAFYDYVGN SPA KGGLFR VGPMNKGDGI AQGWLGHPVF TDAEGRELTV RRLPNFFETF PVILTDADGV IRADIPFRRA ESRYSFEQTG VTVS LYGGE LNGKTFTDPA SVKKYARFAQ QGEPFAFDRE TLGSDGVFRT STRGWFTFGH ACFALLFFFG HIWHGSRTIF RDVFA GVEA DLEEQVEWGN FQKVGDQTTR VQKTV

UniProtKB: UNIPROTKB: A0A9W4EP29

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Macromolecule #8: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 51.545973 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MYSLRRYYRV VTLSSNSYLG GRDQESTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMTLFEVSH FVPEKPMYEQ GLILLPHLA TQGWGVGAGG EVINTFPYFV VGVLHLISSA VLGLGGIYHA VRGPEVLEEY SSFFGYDWKD KNQMTNIIGY H LILLGCGA ...String:
MYSLRRYYRV VTLSSNSYLG GRDQESTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMTLFEVSH FVPEKPMYEQ GLILLPHLA TQGWGVGAGG EVINTFPYFV VGVLHLISSA VLGLGGIYHA VRGPEVLEEY SSFFGYDWKD KNQMTNIIGY H LILLGCGA LLLVFKAMFL GGVYDTWAPG GGDVRIINNP TLNPLVIFGY LLKAPFGGEG WMIGVDNMED IIGGHIWIGL IC IAGGVWH ILTKPFGWAR RAFIWSGEAY LSYSLGALSL MAFIASAFVW FNNTAYPSEF YGPTNAEASQ AQSFVFLVRD QKL GANIGS AQGPTGLGKY LMRSPTGEII FGGETMRFWD FKGPWLEPLR GPNGLDLNKL KNDIQPWQVR RAAEYMTHAP NGSI NSVGG IITEAQGFNY VNPRAWLAAS HFILAFFFLI GHLWHAGRAR AAVAGFEKGI DRETEPVLAM PDLD

UniProtKB: UNIPROTKB: A0A9W4EL13

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Macromolecule #9: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 39.52127 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MTIAVERPQV TRGWFDVLDD WLKRDRFVFV GWSGILLFPC AYLSIGGWLT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLGHSL LFLWGPEAQW DFTRWCQLGG LWAFVALHGA FALIGFCLRQ LEIARLVGIR PYNAIAFTGP IAVFVSVFLM Y PLGQSGWF ...String:
MTIAVERPQV TRGWFDVLDD WLKRDRFVFV GWSGILLFPC AYLSIGGWLT GTTFVTSWYT HGLASSYLEG CNFLTAAVST PANSLGHSL LFLWGPEAQW DFTRWCQLGG LWAFVALHGA FALIGFCLRQ LEIARLVGIR PYNAIAFTGP IAVFVSVFLM Y PLGQSGWF FAPSFGVAGI FRFILFFQGF HNWTLNPFHM MGVAGILGGA LLCAIHGATV ENTLFEDGEG SNTFRAFEPT QA EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMCSIGVV GLAVNLRAYD FVSQELRAAE DPEFETFYTK NIL LNEGIR AWMAPADQPH QNFVFPEEVL PRGNAL

UniProtKB: UNIPROTKB: A0A9W4EL11

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Macromolecule #10: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 10 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 9.344573 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MAGTTGERPF GDIITSVRYW VIHSLTIPAL FIAGWLFVST GLAYDAFGTP RPNEYFTQER QELPIITERQ DSKTQIQQFI AK

UniProtKB: UNIPROTKB: A0A9W4EIR1

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Macromolecule #11: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.994852 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MTNANQNQPI TYPIFTVRWL AVHTLAVPTV FFLGAIAAMQ FIQR

UniProtKB: UNIPROTKB: A0A9W3ZAF8

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Macromolecule #12: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 12 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 7.636935 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MAQRTWLGDR LRPLNSEYGK VAPGWGTTPL MGVFMGLFFV FLLIILQIYN SSLILENVSV DWANLTR

UniProtKB: UNIPROTKB: A0A9W3ZFR1

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Macromolecule #13: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 13 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.414285 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MVTLKIIVNI VVLFFVGLFI FGFLSNDPSR NPKRRDLE

UniProtKB: UNIPROTKB: A0A9W4EN47

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Macromolecule #14: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 14 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 3.914632 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MSGDAKLPLW LIATVAGTGV LVVVGLFFYG AYVGVGSAL

UniProtKB: UNIPROTKB: A0A9W3ZEX7

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Macromolecule #15: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 15 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.979012 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MEAALLLAKL PEAYSIFSPV VDILPVIPVF FLLLAFVWQA AVGFR

UniProtKB: UNIPROTKB: A0A9W4EP73

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Macromolecule #16: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 16 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.581344 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MDRSRNPNKQ PVELNRTSLY LGLLLIFVLG ILFSSYFFN

UniProtKB: UNIPROTKB: A0A9W3ZAC5

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Macromolecule #17: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 17 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.128829 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MEVNDLGFVA SILFVLVPSV FLLILYIQTQ SREGKEG

UniProtKB: UNIPROTKB: A0A9W3ZMZ9

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Macromolecule #18: Photosystem II extrinsic protein O

MacromoleculeName: Photosystem II extrinsic protein O / type: protein_or_peptide / ID: 18 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 30.06477 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString: MKYRALVATF LAFCLSVLTA CSESPSAKDP SLLTYDDIRN TGLAVNCPSL PETARGSIPL DQNASYEITG LCLQPTSYFV KEEPANKRQ EAEFVPGRLL TRFTYSLDQV RGLLKFQPDG SLKFTEKDGI DFQPITVLLP GGEQVPFLFT IKGLVATSQP G LTSINTST ...String:
MKYRALVATF LAFCLSVLTA CSESPSAKDP SLLTYDDIRN TGLAVNCPSL PETARGSIPL DQNASYEITG LCLQPTSYFV KEEPANKRQ EAEFVPGRLL TRFTYSLDQV RGLLKFQPDG SLKFTEKDGI DFQPITVLLP GGEQVPFLFT IKGLVATSQP G LTSINTST DFSGDFNVPS YRGSTFLDPK ARGLASGYDN AVALPATADE EDYVNANVKL ADTKFKAGHI SLQVAKVDGE TG EIAGIFE SEQPSDNDLG AKEAVEVKIR GAFYARIEPK A

UniProtKB: UNIPROTKB: A0A9W3ZRB6

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Macromolecule #19: PsbQ protein

MacromoleculeName: PsbQ protein / type: protein_or_peptide / ID: 19 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 18.64141 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MRFVQIGADF KKTILVMKRY RSILACVLAF VTAFVVGCSS PVAVEPPSYS SIQLEKIQEY KSNIVAIRDR STTELVSYIQ KGDWINIDN FAHGPFGTVL QEMNYVVRNL LPNEQPEARK LSREVFEHLQ DMSEAAAKAD RQQAAISYQE ALKDLDLFLS K FPQV

UniProtKB: UNIPROTKB: A0A9W3ZQ11

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Macromolecule #20: Photosystem II reaction center protein Y

MacromoleculeName: Photosystem II reaction center protein Y / type: protein_or_peptide / ID: 20 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.189124 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MDLDLRIVVV LLPLIVAGGW ALFKIGSAAI SQAQAFMKK

UniProtKB: UNIPROTKB: A0A9W3ZG21

+
Macromolecule #21: LPP1

MacromoleculeName: LPP1 / type: protein_or_peptide / ID: 21 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.017944 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
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) ...String:
(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)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #22: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 22 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 3.439182 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MESVAYILVL TLALGVLFFA IAFREPPRIG K

UniProtKB: UNIPROTKB: A0A9W4EP38

+
Macromolecule #23: PsbU

MacromoleculeName: PsbU / type: protein_or_peptide / ID: 23 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 10.733153 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
ELNKADAKLG TEFGKKLDLN NSSIREFRQY PGMFPTLAKM IIDAAPYDSV QEVLEIPGLT DAQKEIIERY IGEFTITPVE PILQEGDFR LNTGVY

+
Macromolecule #24: Photosystem II extrinsic protein V

MacromoleculeName: Photosystem II extrinsic protein V / type: protein_or_peptide / ID: 24 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 18.16577 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MLKRYIWLAV ATVFFTFQMW VGNANALELT EELRTFPINA QGDTAVLSLK EIKKGQQVFN AACAQCHALG VTKTNPDVNL SPEALALAT PPRDNIAALV DYIKNPTTYD GFVEISELHP SLKSSDIFPK MRNISEDDLY NVAGYILLQP KVRGEQWGGG K YLR

UniProtKB: UNIPROTKB: A0A9W4ELM7

+
Macromolecule #25: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 25 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 5.427645 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MHSKDLIKMT PSLMNFFYSL LAGLLIIVVP ATVGLIFISQ KDKIIRRS

UniProtKB: UNIPROTKB: A0A9W3ZPA1

+
Macromolecule #26: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 26 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 4.692648 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MDFITNLFSN VNFELIAQLL MLSLIVIAGP VVIVLLAFRG GDL

UniProtKB: UNIPROTKB: A0A9W3ZL09

+
Macromolecule #27: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 27 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 6.84835 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MLTLLFQVLL AALVIVSFLM IVAVPVAYAS PQNWSQSKPL IFIGSGLWAV LVILVGVFNY LVV

UniProtKB: UNIPROTKB: A0A9W3ZFP8

+
Macromolecule #28: LPP2

MacromoleculeName: LPP2 / type: protein_or_peptide / ID: 28 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 15.788175 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MLAIGKLFGR SKKSDYFLEF DEAKGTTAEP SPTVAPKAEA PKAEAPKAEA PKAEAPKAEA PKAEKPEKTK KSVAKKSPEA AKANVAATP APAAVAKVAS SSAPLNGGMS KTPEGMTFAT DYLLPKSTAN RRRPGPNMNM FRDMARQMSS K

UniProtKB: UNIPROTKB: A0A9W3ZJ52

+
Macromolecule #29: Allophycocyanin beta-18 subunit

MacromoleculeName: Allophycocyanin beta-18 subunit / type: protein_or_peptide / ID: 29 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 18.446771 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MRDAVTSLIK NYDITGRYLD RDAIDSLKSY FVTGTARVQA AATITANAAE LVKQAASQLF GDLPELIRPG GNAYTTRRYA ACLRDMDYY LRYATYALVA GDTDVLDERV LQGLRETYNS LGVPIGPTVV GIGILKDLAT EKVQAAGIEV GAYLEQPFDH L ISELSETD V

UniProtKB: UNIPROTKB: A0A9W3ZN25

+
Macromolecule #30: Allophycocyanin-B alpha subunit

MacromoleculeName: Allophycocyanin-B alpha subunit / type: protein_or_peptide / ID: 30 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 18.022709 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MTVVSQVILK ADDELRYPTT GELKNISDFL KTGEQRLRIV DTLTENEKKI VDRASAQLWK KRPDFIAPGG NAAGQRERSL CLRDYGWYL RVITYGILSG DKDPIESIGL IGVKEMYNSL GVPMPGMVEA IRCLKEASLA LLDDEDAKEA APYFDFIIQA M S

UniProtKB: UNIPROTKB: A0A9W3ZH43

+
Macromolecule #31: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 31 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 17.616848 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MKTPLTEAVS IADSQGRFLS STEIQVAFGR FRQAKAGLEA AKALTSKADS LISGAAQAVY NKFPYTTQMQ GPNYAADQRG KDKCARDIG YYLRMVTYCL IAGGTGPMDE YLIAGIDEIN RTFELSPSWY IEALKYIKAN HGLSGDAAVE ANSYLDYAIN A LS

+
Macromolecule #32: Phycocyanin beta subunit

MacromoleculeName: Phycocyanin beta subunit / type: protein_or_peptide / ID: 32 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Arthrospira sp. FACHB-439 (bacteria)
Molecular weightTheoretical: 18.062441 KDa
Recombinant expressionOrganism: Arthrospira sp. FACHB-439 (bacteria)
SequenceString:
MFDAFTKVVS QADTRGEMLS TAQIDALSQM VAESNKRLDS VNRITSNAST IVSNAARSLF AEQPQLIAPG GNAYTSRRMA ACLRDMEII LRYVTYAVFA GDASVLEDRC LNGLRETYLA LGTPGSSVAV GVGKMKEAAL AIVNDPAGIT PGDCSALASE I AGYFDRAA AAVS

UniProtKB: Phycocyanin beta subunit

+
Macromolecule #33: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 33 / Number of copies: 348 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

+
Macromolecule #34: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 34 / Number of copies: 6 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #35: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 35 / Number of copies: 12 / Formula: CL
Molecular weightTheoretical: 35.453 Da

+
Macromolecule #36: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 36 / Number of copies: 210 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #37: 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: 37 / Number of copies: 12 / 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 #38: 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: 38 / Number of copies: 27 / 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 #39: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 39 / Number of copies: 48 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #40: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 40 / Number of copies: 54 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #41: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 41 / Number of copies: 6 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

+
Macromolecule #42: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 42 / Number of copies: 27 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #43: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 43 / Number of copies: 60 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #44: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 44 / Number of copies: 24 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #45: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 45 / Number of copies: 12 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #46: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 46 / Number of copies: 6 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #47: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 47 / Number of copies: 12 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #48: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 48 / Number of copies: 18 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 6.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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