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- EMDB-30511: Structural insights into a dimeric Psb27-photosystem II complex f... -

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Basic information

Entry
Database: EMDB / ID: EMD-30511
TitleStructural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus
Map dataPSII-Psb27
Sample
  • Complex: PSII-Psb27
    • Protein or peptide: x 16 types
  • Ligand: x 14 types
Function / homology
Function and homology information


photosystem II stabilization / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding ...photosystem II stabilization / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
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 PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX ...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 PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / 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 CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / 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.
Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L ...Photosystem II CP47 reaction center protein / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsPi X / Huang G / Xiao Y
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium .
Authors: Guoqiang Huang / Yanan Xiao / Xiong Pi / Liang Zhao / Qingjun Zhu / Wenda Wang / Tingyun Kuang / Guangye Han / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular ...Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a deletion mutant (ΔPsbV) of the cyanobacterium , solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII.
History
DepositionSep 9, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7czl
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30511.png

Downloads & links

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Map

FileDownload / File: emd_30511.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSII-Psb27
Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.12535547 - 0.2267318
Average (Standard dev.)0.0009973536 (±0.008977375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 313.5696 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30654166666671.30654166666671.3065416666667
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z313.570313.570313.570
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1250.2270.001

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Supplemental data

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Sample components

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Entire : PSII-Psb27

EntireName: PSII-Psb27
Components
  • Complex: PSII-Psb27
    • 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 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 protein Z
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Psb27
    • Protein or peptide: Photosystem II reaction center protein X
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: BICARBONATE IONBicarbonate
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM IONCalcium
  • Ligand: FE (II) ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CHLORIDE IONChloride

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Supramolecule #1: PSII-Psb27

SupramoleculeName: PSII-Psb27 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 35.894949 KDa
SequenceString: SANLWERFCN WVTSTDNRLY VGWFGVIMIP TLLAATICFV IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVVPSSNAI GLHFYPIWE AASLDEWLYN GGPYQLIIFH FLLGASCYMG RQWELSYRLG MRPWICVAYS APLASAFAVF LIYPIGQGSF S DGMPLGIS ...String:
SANLWERFCN WVTSTDNRLY VGWFGVIMIP TLLAATICFV IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVVPSSNAI GLHFYPIWE AASLDEWLYN GGPYQLIIFH FLLGASCYMG RQWELSYRLG MRPWICVAYS APLASAFAVF LIYPIGQGSF S DGMPLGIS GTFNFMIVFQ AEHNILMHPF HQLGVAGVFG GALFCAMHGS LVTSSLIRET TETESANYGY KFGQEEETYN IV AAHGYFG RLIFQYASFN NSRSLHFFLA AWPVVGVWFT ALGISTMAFN LNGFNFNHSV IDAKGNVINT WADIINRANL GME VMHE

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 56.096758 KDa
SequenceString: GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS ...String:
GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS DPYGLTGSVQ PVAPEWGPDG FNPYNPGGVV AHHIAAGIVG IIAGLFHILV RPPQRLYKAL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDSS YFQQEINRRV QASLASGATL EEAWSAIPEK LAFYDYIGNN PAK GGLFRT GPMNKGDGIA QAWKGHAVFR NKEGEELFVR RMPAFFESFP VILTDKNGVV KADIPFRRAE SKYSFEQQGV TVSF YGGEL NGQTFTDPPT VKSYARKAIF GEIFEFDTET LNSDGIFRTS PRGWFTFAHA VFALLFFFGH IWHGARTLFR DVFSG IDPE LSPEQVEWGF YQKVGDVTTR R

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 48.648688 KDa
SequenceString: DQESSGFAWW AGNARLINLS GKLLGAHVAH AGLIVFWAGA MTLFELAHFI PEKPMYEQGL ILIPHIATLG WGVGPGGEVV DTFPFFVVG VVHLISSAVL GFGGVYHAIR GPETLEEYSS FFGYDWKDKN KMTTILGFHL IVLGIGALLL VAKAMFFGGL Y DTWAPGGG ...String:
DQESSGFAWW AGNARLINLS GKLLGAHVAH AGLIVFWAGA MTLFELAHFI PEKPMYEQGL ILIPHIATLG WGVGPGGEVV DTFPFFVVG VVHLISSAVL GFGGVYHAIR GPETLEEYSS FFGYDWKDKN KMTTILGFHL IVLGIGALLL VAKAMFFGGL Y DTWAPGGG DVRVITNPTL DPRVIFGYLL KSPFGGEGWI VSVNNLEDVV GGHIWIGLIC IAGGIWHILT TPFGWARRAF IW SGEAYLS YSLGALSMMG FIATCFVWFN NTVYPSEFYG PTGPEASQAQ AMTFLIRDQK LGANVGSAQG PTGLGKYLMR SPT GEIIFG GETMRFWDFR GPWLEPLRGP NGLDLNKIKN DIQPWQERRA AEYMTHAPLG SLNSVGGVAT EINSVNFVSP RSWL ATSHF VLAFFFLVGH LWHAGRARAA AAGFEKGIDR ESEPVLSMPS L

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 38.005484 KDa
SequenceString: GWFDILDDWL KRDRFVFVGW SGILLFPCAY LALGGWLTGT TFVTSWYTHG LASSYLEGCN FLTVAVSTPA NSMGHSLLLL WGPEAQGDF TRWCQLGGLW TFIALHGAFG LIGFMLRQFE IARLVGVRPY NAIAFSAPIA VFVSVFLIYP LGQSSWFFAP S FGVAAIFR ...String:
GWFDILDDWL KRDRFVFVGW SGILLFPCAY LALGGWLTGT TFVTSWYTHG LASSYLEGCN FLTVAVSTPA NSMGHSLLLL WGPEAQGDF TRWCQLGGLW TFIALHGAFG LIGFMLRQFE IARLVGVRPY NAIAFSAPIA VFVSVFLIYP LGQSSWFFAP S FGVAAIFR FLLFFQGFHN WTLNPFHMMG VAGVLGGALL CAIHGATVEN TLFQDGEGAS TFRAFNPTQA EETYSMVTAN RF WSQIFGI AFSNKRWLHF FMLFVPVTGL WMSAIGVVGL ALNLRSYDFI SQEIRAAEDP EFETFYTKNL LLNEGIRAWM APQ DQPHEN FVFPEEVLPR GNA

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 7.495497 KDa
SequenceString:
WVIHSITIPA LFIAGWLFVS TGLAYDVFGT PRPDSYYAQE QRSIPLVTDR FEAKQQVETF LEQLK

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.461166 KDa
SequenceString:
PIFTVRWVAV HTLAVPTIFF LGAIAAMQFI Q

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 6.986271 KDa
SequenceString:
ARRTWLGDIL RPLNSEYGKV APGWGTTPLM AVFMGLFLVF LLIILEIYNS TLILDGVNVS WK

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.923706 KDa
SequenceString:
METLKITVYI VVTFFVLLFV FGFLSGDPAR NPKR

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.101911 KDa
SequenceString:
KLPEAYAIFD PLVDVLPVIP VLFLALAFVW QAAVGFR

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.299044 KDa
SequenceString:
MEPNPNRQPV ELNRTSLYLG LLLILVLALL FSSYFFN

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.678338 KDa
SequenceString:
MEVNQLGLIA TALFVLVPSV FLIILYVQTE SQQ

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.620369 KDa
SequenceString:
METITYVFIF ACIIALFFFA IFFREPPRIT

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Macromolecule #13: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 6.766187 KDa
SequenceString:
MTILFQLALA ALVILSFVMV IGVPVAYASP QDWDRSKQLI FLGSGLWIAL VLVVGVLNFF VV

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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: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.228035 KDa
SequenceString:
EVIAQLTMIA MIGIAGPMII FLLAVRRGNL

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Macromolecule #15: Psb27

MacromoleculeName: Psb27 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 12.234814 KDa
SequenceString:
TGLTGNFRED TLALISSLRE AIALPENDPN KKAAQAEARK KLNDFFALYR RDDSLRSLSS FMTMQTALNS LAGHYSSYPN RPLPEKLKA RLEQEFKQVE LALDREAKS

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Macromolecule #16: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.19103 KDa
SequenceString:
TITPSLKGFF IGLLSGAVVL GLTFAVLIAI SQIDKVQRSL

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Macromolecule #17: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 17 / Number of copies: 70 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #18: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 18 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

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Macromolecule #19: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA...

MacromoleculeName: 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
type: ligand / ID: 19 / Number of copies: 4 / Formula: PQ9
Molecular weightTheoretical: 612.967 Da
Chemical component information

ChemComp-PQ9:
5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE

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Macromolecule #20: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 20 / Number of copies: 22 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #21: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 21 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #22: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 22 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #23: 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: 23 / Number of copies: 6 / 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 #24: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 24 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

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Macromolecule #25: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 25 / Number of copies: 14 / Formula: MGE
Molecular weightTheoretical: 688.972 Da
Chemical component information

ChemComp-MGE:
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE

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Macromolecule #26: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 26 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #27: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 27 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 29 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #30: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 30 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87473

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