EMDB-37414: Structure of PSII-ACPII supercomplex from cryptophyte algae

Basic information

Entry

Database: EMDB / ID: EMD-37414

• Title: Structure of PSII-ACPII supercomplex from cryptophyte algae

Sample

• Complex: Structure of PSII-ACPII supercomplex from cryptophyte algae
  • Protein or peptide: x 30 types
• Ligand: x 17 types

• Keywords: Photosystem II / PHOTOSYNTHESIS

Function / homology

Function:

thylakoid membrane / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plastid / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / heme binding / metal ion binding

Domain/homology:

Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / 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 CP43 reaction centre protein superfamily / 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 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 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 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 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily

Component:

Photosystem II cytochrome c550 / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit beta / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Photosystem II reaction center protein X / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein K / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center M

• Biological species: Chroomonas placoidea (eukaryote)
• Method: single particle reconstruction / cryo EM / Resolution: 2.47 Å
• Authors: Li XY / Mao ZY / Shen JR / Han GY

Funding support

China, 1 items

Organization	Grant number	Country
Chinese Academy of Sciences	YSBR-004	China

• Citation: Journal: Nat Commun / Year: 2024; Title: Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea.; Authors: Zhiyuan Mao / Xingyue Li / Zhenhua Li / Liangliang Shen / Xiaoyi Li / Yanyan Yang / Wenda Wang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / ; Abstract: Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery.

History

Deposition	Sep 8, 2023	-
Header (metadata) release	Jun 5, 2024	-
Map release	Jun 5, 2024	-
Update	Jun 5, 2024	-
Current status	Jun 5, 2024	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_37414.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.04 Å

Density

Contour Level	By AUTHOR: 0.253
Minimum - Maximum	-0.33255997 - 1.3070133
Average (Standard dev.)	-0.0003721935 (±0.030487914)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 512 512 512 Spacing 512 512 512
Cell	A=B=C: 532.48 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_37414_half_map_1.map

Half map: #1

• File: emd_37414_half_map_2.map

Sample components

Entire : Structure of PSII-ACPII supercomplex from cryptophyte algae

• Entire: Name: Structure of PSII-ACPII supercomplex from cryptophyte algae

Components

• Complex: Structure of PSII-ACPII supercomplex from cryptophyte algae
  • Protein or peptide: Photosystem II reaction center M
  • Protein or peptide: ACPII-1
  • Protein or peptide: ACPII-2
  • Protein or peptide: ACPII-3
  • Protein or peptide: ACPII-4
  • Protein or peptide: ACPII-5
  • Protein or peptide: ACPII-6
  • Protein or peptide: Photosystem II protein D1
  • 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 O
  • Protein or peptide: Photosystem II reaction center protein Q
  • Protein or peptide: Photosystem II reaction center protein R
  • Protein or peptide: CCPII-S
  • Protein or peptide: Photosystem II reaction center protein T
  • Protein or peptide: Photosystem II reaction center protein U
  • Protein or peptide: Photosystem II cytochrome c550
  • 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: Photosystem II CP47 reaction center protein
  • Protein or peptide: Photosystem II CP43 reaction center protein
  • Protein or peptide: Photosystem II reaction center protein G
  • Protein or peptide: Photosystem II reaction center protein L
  • Protein or peptide: Photosystem II reaction center protein W
• Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
• Ligand: CHLOROPHYLL A
• Ligand: Chlorophyll c2
• Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
• Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
• Ligand: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
• Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
• Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
• Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
• Ligand: CA-MN4-O5 CLUSTER
• Ligand: PHEOPHYTIN A
• Ligand: CHLORIDE 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: BICARBONATE ION
• Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
• Ligand: FE (II) ION
• Ligand: PROTOPORPHYRIN IX CONTAINING FE

Supramolecule #1: Structure of PSII-ACPII supercomplex from cryptophyte algae

• Supramolecule: Name: Structure of PSII-ACPII supercomplex from cryptophyte algae; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
• Source (natural): Organism: Chroomonas placoidea (eukaryote)

Macromolecule #1: Photosystem II reaction center M

• Macromolecule: Name: Photosystem II reaction center M / type: protein_or_peptide / ID: 1 ; Details: Author stated: We did not find the sequence of chain m,M in the transcriptome of Chroomonas placoidea, so the sequence in Guillardia theta (strain CCMP2712) (tax id 905079) was used.; Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 11.880879 KDa

Sequence

String:

MQRLALLVAA TIASAAAFAP TPALTGLRQQ APLCSGNKLS AACRAPRAAK PAMTMSLAET TNQAMLLAEG GMNVSVAAYL AVLLGTFIP VVFLLTLYIQ SESRKAAETG SEGDKF

UniProtKB: Photosystem II reaction center M

Macromolecule #2: ACPII-1

• Macromolecule: Name: ACPII-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 25.151223 KDa

Sequence

String:

KMLRLSILAA CLAAAQAFTS PAALLRPSTR AAVSRGPSMQ LYKDGIIQGL GVEAIPGAGR PANLDGTLVG DVGFDPLGFS NWLDLRWAR EAEIKHGRVA MLAATGMIVQ DAYKFPGFEG EFGGAAMMKL HNLAVEQGAM QQLLLWLGLL EIISGVPAII Q TLNGSERQ PGDFGFDPLN CGANPDTLAR RQLTELKNGR LAMIAVGGMV HHYLLVGRGP IEFITNIPNF KNPLPPF

Macromolecule #3: ACPII-2

• Macromolecule: Name: ACPII-2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 23.471201 KDa

Sequence

String:

AMLRVALIAA ILASASAFAP MGSLGLVKSA RSGAAISPRM QSGDFSAAVP FLKRPSNLDG TLAGDVGFDP LGFSDVFDLR VLREAELKH GRFAMLAVLG FLVQEVYTFP FFPKMAPVDA HDYFVTQGGG SQIIFWISFV EIFGVVALFE LIQGKRDAGD F AFDPLGLG KDEATLARYK VAEIKHARLA MIAIGGFIHQ FWVTKQTVLE QLGNFQSLA

Macromolecule #4: ACPII-3

• Macromolecule: Name: ACPII-3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 24.05502 KDa

Sequence

String:

ITHSRMLRTA ILALCVAGAS AFTASPALYK SASRKAAVSG MKMQDRSYAM PFLSRPPALD GSMAGDVGFD PLGFSNYFDL KWLREAELK HGRVCMLGCL GFLVQEQANL PLPGFDNKLA TEAFFSVPAG GLWQIFFSLG AIEIITNKGK LTPGSMFTGG R APGDLDFD PLNLSVDETA LRRFELAELK HARLAMIGLG GMLHQMLLTK QAPIEQLTNF KSLA

Macromolecule #5: ACPII-4

• Macromolecule: Name: ACPII-4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 23.734623 KDa

Sequence

String:

AVVLAACVAS AAAFAPGASV LPRAAARATS TKGPSMQLLP LYGEGKLQGP GTQAIPGSEP PPALDGTWVG DVGFDPLGFS RVIDMRWLR EAELKHGRVC MLAATGMIVQ DIALFPGVTK TFGPAKITAL HDVAVKQGSM QQLLVWLGFL EIFGFVAIVQ M LQGSGRQP GDFGFDPLNC GANTDTLARR QLVELKNGRL AMIATGGMIH HFFLTGKGPI EFITTLGA

Macromolecule #6: ACPII-5

• Macromolecule: Name: ACPII-5 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 23.762242 KDa

Sequence

String:

ACASAAAFAP GAMPSIGKAP RAVSKTAPRM AVFPGQFSDS VPFLKQPTNL DGSYVGDVGF DPLGFSDVFD IRVLREAELK HGRIAMLAT LGMVVQEAYT FPFFDKVLPI PAHDVIVKSG GMSQILLWTS FAEIFGGIAL FQTIQGKRAP GDYSFDPLNL S ANDLEKRE RYALAEIKHS RLAMLAFSGM VHQYFITNQG VIEQINNFRP INGFPDATFS

Macromolecule #7: ACPII-6

• Macromolecule: Name: ACPII-6 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 23.923801 KDa

Sequence

String:

PAMFRAALLL ACLASASAFA PGSLMMPKSA TRAAISRGPR MQANDDLAVP FLERPPMLDG SYAGDIGFDP VGFSNYFDLR WLREAELKH GRVCMLGVVG FLVQEFVTLP MFSNGVTPVD DFFVVPATGL WQIFFTIGFV EAFSNGFKLT PSDMFADDRA P GDLGFDPL GCGKDPAALA RRQLVEVKNG RLAMIAFGGM LHQQLLTKQG VIEQLTNFKA IM

Macromolecule #8: Photosystem II protein D1

• Macromolecule: Name: Photosystem II protein D1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 39.59091 KDa

Sequence

String:

MTATLERRES ASAWERFCSW ITSTDNRLYI GWFGVLMIPT LLTATTVYII AFVAAPPVDI DGIREPVAGS LLYGNNIITG AVIPSSASI GIHFYPIWEA ASLDEWLYNG GPYQLIVDHF LLGVCGWIGR EWEFSYRLGM RPWISVAFTA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMLVFQA EHNILMHPFH QLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLGL WPVVGIWFTA LGVMTMAFNL NGFNFNQSVV DSQGRVINTW ADI LNRANL GMEVMHERNA HNFPLDLAAG ESLPVALTAP AVNG

UniProtKB: Photosystem II protein D1

Macromolecule #9: Photosystem II D2 protein

• Macromolecule: Name: Photosystem II D2 protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 39.216812 KDa

Sequence

String:

MTIAIGQEEG RGWFDLIDDW LKRDRFVFVG WSGLLLFPTS YLSIGGWFTG TTFVTSWYTH GLASSYLEGC NFFTAAVSTP ANSMGHSLL LLWGPEAQGD FTRWCQIGGL WAFCALHGSF ALIGFCLRQF EIARLVGIRP YNAIAFSGPI AIFVSVFLMY P LGQASWFF APSLGVAAIF RFLLFIQGFH NFTLNPFHMM GVAGILGAAL LCAIHGATVQ NTIFEDGDAA NTFRAFTPTQ AE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPLAG LWTSAIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN ILL NEGIRS WMAAQDQPHE NFIFPEEVLP RGNAL

UniProtKB: Photosystem II D2 protein

Macromolecule #10: Cytochrome b559 subunit alpha

• Macromolecule: Name: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 9.505693 KDa

Sequence

String:

MSGGSTGERP FSDIITSIRY WIIHSITIPA LYVAGWLFVS TGLAYDIFGT PRPNEYFTQD RQQVPLVNDR FSAKQELEDL TKGL

UniProtKB: Cytochrome b559 subunit alpha

Macromolecule #11: Cytochrome b559 subunit beta

• Macromolecule: Name: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 4.845769 KDa

Sequence

String:

MSKIQQPVSY PIFTFRWLAI HGLAVPTVFF LGAITSMQFI QR

UniProtKB: Cytochrome b559 subunit beta

Macromolecule #12: Photosystem II reaction center protein H

• Macromolecule: Name: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 7.519887 KDa

Sequence

String:

MALRTRLGEL LRPLNSEYGK VAPGWGTTPI MGFVMLLFFL FLLIILQIYN SSLIIENVDV DWASLGS

UniProtKB: Photosystem II reaction center protein H

Macromolecule #13: Photosystem II reaction center protein I

• Macromolecule: Name: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 4.424081 KDa

Sequence

String:

MFTLKIVVYT TVTFFVSLFT FGFLSNDASR NPNRKDLE

UniProtKB: Photosystem II reaction center protein I

Macromolecule #14: Photosystem II reaction center protein J

• Macromolecule: Name: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 3.964609 KDa

Sequence

String:

MASTGRIPLW LIATVGGTLA LTVVGIFFYG SYSGVGSSL

UniProtKB: Photosystem II reaction center protein J

Macromolecule #15: Photosystem II reaction center protein K

• Macromolecule: Name: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 5.005114 KDa

Sequence

String:

MEAILLIAKL PEAYAVFKPI IDVAPVIPVF FLLLAFVWQA AVGFR

UniProtKB: Photosystem II reaction center protein K

Macromolecule #16: Photosystem II reaction center protein O

• Macromolecule: Name: Photosystem II reaction center protein O / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 34.995547 KDa

Sequence

String:

LAMARLAILL GLVASAAAFT GPAVLPLKAS NRAAACSVTM QDNSLAKKAA GIAAIPLSFL LGVNAANAIT TEDIRGLTYS QVKGTGLAN RCPEVSEQNA GGTIKFADDK KYKVTELCLE PKSFQIEEEV TKRRGETKKE FVDTKLMTRA TYSLTGIEGP I VFKDGGLT FLEKGGIDYA ATTVQLPGGE RVPFLFTIKE LEGKFSSSQV SAGTELGGNF KTPSYRTGLF LDPKGRGGTT GY DMAVALP GLEADGGEGQ DELFAETNKV FQVTDGSIEM AFNRVDGTNG EFSGVFVSEQ LSDTDMGSKA PKKVLLKGIV FGK IEEQTG DEDY

Macromolecule #17: Photosystem II reaction center protein Q

• Macromolecule: Name: Photosystem II reaction center protein Q / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 1.805216 KDa

Sequence

String:

(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)

Macromolecule #18: Photosystem II reaction center protein R

• Macromolecule: Name: Photosystem II reaction center protein R / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 2.230741 KDa

Sequence

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)

Macromolecule #19: CCPII-S

• Macromolecule: Name: CCPII-S / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 30.531848 KDa

Sequence

String:

DHKRSRMMKS LALAAVGLAV GAEAFAPTPM VGGAKLALRT SSTRSVATVG PKMAMDVNAI VEGAQYLTAA VPNVPFVDEI TGEPQGLTA PIVHFGSVIS LWLLFALPVW SAAYKAAGAD TAEWVGVSQV TEDAPGIGLY GKYAPEYDGP TFREGLEYVL S FAWKPPIL IAWKPRADLD RAMMDPARDT VVSSLYKSLG GALDKTAVYD EEDQLLILSD METFPETELG RRRVAQAEAA GW FTGNPSF GKSLIEYSEE TKKGMREPGT VSISAKELAA LRAEAAKK

Macromolecule #20: Photosystem II reaction center protein T

• Macromolecule: Name: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 3.664447 KDa

Sequence

String:

METLVYVFLL AGTLGVIFFA VFFRDPPRIA KK

UniProtKB: Photosystem II reaction center protein T

Macromolecule #21: Photosystem II reaction center protein U

• Macromolecule: Name: Photosystem II reaction center protein U / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 15.962294 KDa

Sequence

String:

LIAALAVSAS AFSPAVPALR TAPQACGITM QAESVDRRGF LGALGAAVVA APLAASANVE YPNVPYLGGS DIIDVNNANV RVYTRLPGM YPAIAKKIIK RAPYKDINEM LEKGDFTAAE KDILDKYLPN LTALEPAPEY VIDNINNGLY R

Macromolecule #22: Photosystem II cytochrome c550

• Macromolecule: Name: Photosystem II cytochrome c550 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 17.708234 KDa

Sequence

String:

MLKRFSSLNI ILGMLLVSFV ASPVHATDLD ENTRTVPLDS SGTTVILTPE QVKRGKRLFN SSCGNCHVGG ITKTNPNLGL EPDALSLAT PARDNIDALV DYMKNPTTYD GLESIAELHP SVKSADIFPK MRSLSDEDLF AIGGHILLQP KLSSEKWGGG K IYY

UniProtKB: Photosystem II cytochrome c550

Macromolecule #23: Photosystem II reaction center X protein

• Macromolecule: Name: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 4.149939 KDa

Sequence

String:

MTPSLSAFIN SLLLGLFVVV IPIGAALFLV SQSDRVTRT

UniProtKB: Photosystem II reaction center protein X

Macromolecule #24: Photosystem II reaction center protein Ycf12

• Macromolecule: Name: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 3.763581 KDa

Sequence

String:

MFNPTTLFQL IALFLVITSG PAIIVLIAFR RGNL

UniProtKB: Photosystem II reaction center protein Psb30

Macromolecule #25: Photosystem II reaction center protein Z

• Macromolecule: Name: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 6.57399 KDa

Sequence

String:

MVGLLQILVS ILILLSFALV VGVPVILVSP GEWEKSKGLV YSAAGLWFGL VIVIAAFNSF VI

UniProtKB: Photosystem II reaction center protein Z

Macromolecule #26: Photosystem II CP47 reaction center protein

• Macromolecule: Name: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 56.354172 KDa

Sequence

String:

MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMARIG VTDSWGGWSV TGESVANPG FWSFEGVALA HIGLSGLLFL AAVWHWVYWD LELFRDPRTG NPALDLPKIF GIHLLLSGVL CFGFGAFHVT G AWGPGIWV SDAYGITGKV QPVAPAWGAE GFNPFNPSGV ASHHIAAGIL GFLAGIFHIA VRPPQRLYRA LRMGNIETVL SS SIAAVFW SAFITTGTMW YGSATTPIEL FGPTRYQWDS GYFQQEIERR VENSLNEGLN LSEAWSRIPD KLAFYDYIGN NPA KGGLFR AGPMNKGDGI AEAWLGHPIF QDKEGKELTV RRMPAFFETF PVILVDKDGI IRADIPFRRA ESKYSIEQVG VTVS FYGGK LNGQVFKDAP TVKKYARKAQ LGEVLEFDRT TLESDGVFRS SPRGWYTFGH ANFALLFFLG HLWHGSRTLF RDVFS GIGA EVTEQVEFGA FQKLGDRSTK KQGAV

UniProtKB: Photosystem II CP47 reaction center protein

Macromolecule #27: Photosystem II CP43 reaction center protein

• Macromolecule: Name: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 50.508488 KDa

Sequence

String:

METPFNSSLS VAGRDIESTG FAWWSGNSRL INVSGKLLGA HVAHAGLMVF WCGAMTLFEV AHYIPEKPLY EQGLILLPHL AVLGWGVGP GGEIIDIYPY FVVGVLHLIS SAVLGFGGVY HSLIGPDTLE ESFPAFGYDW RDKNKITTIL GIHLIVLGIG A FLLVIKAM YVGGIYDTWA PGGGDVRIID SPTLNPGVIF GYVLKSPWGG DGWIVSVNNM EDLVGGHIWI GIICIVGGFW HI FTKPFAW ARRAYVWSGE AYLSYSLVAV SLMGFIASQY SWYNNTAYPS EFYGPTGPEA SQSQAFTFLV RDQRLGANVS SAQ GPTGLG KYLMRSPSGE IILGGETQRF WDLRAPWIEP LRGPNGLDLN KIKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINSV NYVSPRSWLT CAHFFLGFAF YIGHLWHAGR ARAAAAGFEK GINRENEPTL SLRPID

UniProtKB: Photosystem II CP43 reaction center protein

Macromolecule #28: Photosystem II reaction center protein G

• Macromolecule: Name: Photosystem II reaction center protein G / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 5.464728 KDa

Sequence

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)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

Macromolecule #29: Photosystem II reaction center protein L

• Macromolecule: Name: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 29 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 4.363087 KDa

Sequence

String:

MSGPNPNKQP VELNRTSLFW GLLLIFVLAV LFSSYFFN

UniProtKB: Photosystem II reaction center protein L

Macromolecule #30: Photosystem II reaction center protein W

• Macromolecule: Name: Photosystem II reaction center protein W / type: protein_or_peptide / ID: 30 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Chroomonas placoidea (eukaryote)
• Molecular weight: Theoretical: 11.994986 KDa

Sequence

String:

SKVLFLALCL VAGASAFNAP APMALRASKT AMTMKAEGPM PKLAKALAPA IAAANIAIAS PVFAEGTGEA LGIDDTRLIV PVILIPVIT FILYAGFASE QDNEDFFDTY DQRRK

Macromolecule #31: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

• Macromolecule: Name: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene; type: ligand / ID: 31 / Number of copies: 24 / Formula: 8CT
• Molecular weight: Theoretical: 536.873 Da

Chemical component information

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

Macromolecule #32: CHLOROPHYLL A

• Macromolecule: Name: CHLOROPHYLL A / type: ligand / ID: 32 / Number of copies: 208 / Formula: CLA
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

Macromolecule #33: Chlorophyll c2

• Macromolecule: Name: Chlorophyll c2 / type: ligand / ID: 33 / Number of copies: 12 / Formula: KC2
• Molecular weight: Theoretical: 608.926 Da

Chemical component information

ChemComp-KC2:
Chlorophyll c2

Macromolecule #34: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

• Macromolecule: Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol; type: ligand / ID: 34 / Number of copies: 42 / Formula: II0
• Molecular weight: Theoretical: 564.84 Da

Chemical component information

ChemComp-II0:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol

Macromolecule #35: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

• Macromolecule: Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol; type: ligand / ID: 35 / Number of copies: 4 / Formula: II3
• Molecular weight: Theoretical: 566.856 Da

Chemical component information

ChemComp-II3:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol

Macromolecule #36: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

• Macromolecule: Name: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol; type: ligand / ID: 36 / Number of copies: 10 / Formula: IHT
• Molecular weight: Theoretical: 550.856 Da

Chemical component information

ChemComp-IHT:
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol

Macromolecule #37: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

• Macromolecule: Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 37 / Number of copies: 20 / Formula: LMG
• Molecular weight: Theoretical: 787.158 Da

Chemical component information

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

Macromolecule #38: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

• Macromolecule: Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 38 / Number of copies: 18 / Formula: LHG
• Molecular weight: Theoretical: 722.97 Da

Chemical component information

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

Macromolecule #39: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

• Macromolecule: Name: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL; type: ligand / ID: 39 / Number of copies: 8 / Formula: SQD
• Molecular weight: Theoretical: 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 #40: CA-MN4-O5 CLUSTER

• Macromolecule: Name: CA-MN4-O5 CLUSTER / type: ligand / ID: 40 / Number of copies: 2 / Formula: OEX
• Molecular weight: Theoretical: 339.827 Da

Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

Macromolecule #41: PHEOPHYTIN A

• Macromolecule: Name: PHEOPHYTIN A / type: ligand / ID: 41 / Number of copies: 4 / Formula: PHO
• Molecular weight: Theoretical: 871.2 Da

Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

Macromolecule #42: CHLORIDE ION

• Macromolecule: Name: CHLORIDE ION / type: ligand / ID: 42 / Number of copies: 2 / Formula: CL
• Molecular weight: Theoretical: 35.453 Da

Macromolecule #43: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

• Macromolecule: Name: 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: 43 / Number of copies: 4 / Formula: PL9
• Molecular weight: Theoretical: 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 #44: BICARBONATE ION

• Macromolecule: Name: BICARBONATE ION / type: ligand / ID: 44 / Number of copies: 2 / Formula: BCT
• Molecular weight: Theoretical: 61.017 Da

Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

Macromolecule #45: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

• Macromolecule: Name: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 45 / Number of copies: 10 / Formula: DGD
• Molecular weight: Theoretical: 949.299 Da

Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

Macromolecule #46: FE (II) ION

• Macromolecule: Name: FE (II) ION / type: ligand / ID: 46 / Number of copies: 2 / Formula: FE2
• Molecular weight: Theoretical: 55.845 Da

Macromolecule #47: PROTOPORPHYRIN IX CONTAINING FE

• Macromolecule: Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 47 / Number of copies: 4 / Formula: HEM
• Molecular weight: Theoretical: 616.487 Da

Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 305400
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD