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- EMDB-30909: Cryo-EM structure of PSII intermediate Psb28-PSII complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30909
TitleCryo-EM structure of PSII intermediate Psb28-PSII complex
Map data
Sample
  • Complex: Cryo-EM structure of PSII intermediate Psb28-PSII complex.
    • Protein or peptide: x 17 types
  • Protein or peptide: x 1 types
  • Ligand: x 13 types
KeywordsPhotosystem II / Cryo-EM / assembly / repair / Psb28 / Tsl0063 / PLANT PROTEIN
Function / homology
Function and homology information


photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction ...photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
: / Photosystem II Psb28, class 1 / Photosystem II Psb28, class 1 superfamily / Psb28 protein / 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 Psb28, class 1 / Photosystem II Psb28, class 1 superfamily / Psb28 protein / 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 PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II 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 protein D1 / Photosystem II assembly factor Psb28 protein / Photosystem II assembly protein Psb34 / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsSui SF / Shen JR
CitationJournal: Nat Plants / Year: 2021
Title: Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063.
Authors: Yanan Xiao / Guoqiang Huang / Xin You / 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 catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. ...Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (Q) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.
History
DepositionJan 18, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dxh
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30909.png

Downloads & links

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Map

FileDownload / File: emd_30909.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.035
Minimum - Maximum-0.14970955 - 0.26054797
Average (Standard dev.)0.0004798068 (±0.0069461353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1500.2610.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of PSII intermediate Psb28-PSII complex.

EntireName: Cryo-EM structure of PSII intermediate Psb28-PSII complex.
Components
  • Complex: Cryo-EM structure of PSII intermediate Psb28-PSII complex.
    • Protein or peptide: Photosystem II reaction center Psb28 protein
    • Protein or peptide: Tsl0063 protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 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 L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: unidentified transmembrane protein
  • Protein or peptide: Photosystem II reaction center protein T
  • Ligand: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
  • Ligand: CHLORIDE ION
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PHEOPHYTIN A
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (II) ION
  • 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: UNKNOWN LIGAND
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: heptyl 1-thio-beta-D-glucopyranoside

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Supramolecule #1: Cryo-EM structure of PSII intermediate Psb28-PSII complex.

SupramoleculeName: Cryo-EM structure of PSII intermediate Psb28-PSII complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11, #13-#18
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)

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Macromolecule #1: Photosystem II reaction center Psb28 protein

MacromoleculeName: Photosystem II reaction center Psb28 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 13.188769 KDa
SequenceString:
MGAMAEIQFI RGINEEVVPD VRLTRARDGS SGQAMFYFDN PKIVQEGNLE VTGMYMVDEE GEIVTRDVNA KFINGQPVAI EATYTMRSP QEWDRFIRFM DRYAASHGLG FQKSENS

UniProtKB: Photosystem II assembly factor Psb28 protein

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Macromolecule #2: Tsl0063 protein

MacromoleculeName: Tsl0063 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 5.943893 KDa
SequenceString:
MRYTTDEGGR LNNFAIEPKV YQAQPWTPQQ KVRAALLVGG GLLLVAGLVA IAVGVS

UniProtKB: Photosystem II assembly protein Psb34

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Macromolecule #3: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 39.792367 KDa
SequenceString: MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF ...String:
MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH QLGVAGVFGG ALFCAMHGSL VTSSLIRETT ETESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WRVVGVWFAA LGISTMAFNL NGFNFNHSVI DAKGNVINTW ADI INRANL GMEVMHERNA HNFPLDLASA ESAPVAMIAP SING

UniProtKB: Photosystem II protein D1

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Macromolecule #4: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 56.068742 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 K

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #5: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 38.404949 KDa
SequenceString: ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI ...String:
ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI FRFLLFFQGF HNWTLNPFHM MGVAGVLGGA LLCAIHGATV ENTLFQDGEG ASTFRAFNPT QAEETYSMVT AN RFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGVV GLALNLRSYD FISQEIRAAE DPEFETFYTK NLLLNEGIRA WMA PQDQPH ENFVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #6: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 9.58084 KDa
SequenceString:
MAGTTGERPF SDIITSVRYW VIHSITIPAL FIAGWLFVST GLAYDVFGTP RPDSYYAQEQ RSIPLVTDRF EAKQQVETFL EQLK

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 5.0679 KDa
SequenceString:
MTSNTPNQEP VSYPIFTVRW VAVHTLAVPT IFFLGAIAAM QFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #8: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 7.227559 KDa
SequenceString:
ARRTWLGDIL RPLNSEYGKV APGWGTTPLM AVFMGLFLVF LLIILEIYNS TLILDGVNVS WKALG

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #9: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.410245 KDa
SequenceString:
METLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKDLE

UniProtKB: Photosystem II reaction center protein I

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.299044 KDa
SequenceString:
MEPNPNRQPV ELNRTSLYLG LLLILVLALL FSSYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #11: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.015688 KDa
SequenceString:
MEVNQLGFIA TALFVLVPSV FLIILYVQTE SQQKSS

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.878728 KDa
SequenceString:
METITYVFIF ACIIALFFFA IFFREPPRIT KK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #13: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.19103 KDa
SequenceString:
TITPSLKGFF IGLLSGAVVL GLTFAVLIAI SQIDKVQRSL

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #14: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 49.20725 KDa
SequenceString: ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGPG GEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG ALLLVAKAMF F GGLYDTWA ...String:
ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGPG GEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG ALLLVAKAMF F GGLYDTWA PGGGDVRVIT NPTLDPRVIF GYLLKSPFGG EGWIVSVNNL EDVVGGHIWI GLICIAGGIW HILTTPFGWA RR AFIWSGE AYLSYSLGAL SMMGFIATCF VWFNNTVYPS EFYGPTGPEA SQAQAMTFLI RDQKLGANVG SAQGPTGLGK YLM RSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KIKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVATEINSVN FVSP RSWLA TSHFVLAFFF LVGHLWHAGR ARAAAAGFEK GIDRESEPVL SMPSLD

UniProtKB: Photosystem II CP43 reaction center protein

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 5.028083 KDa
SequenceString:
MIDALVLVAK LPEAYAIFDP LVDVLPVIPV LFLALAFVWQ AAVGFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #16: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 6.766187 KDa
SequenceString:
MTILFQLALA ALVILSFVMV IGVPVAYASP QDWDRSKQLI FLGSGLWIAL VLVVGVLNFF VV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #17: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.228035 KDa
SequenceString:
EVIAQLTMIA MIGIAGPMII FLLAVRRGNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #18: unidentified transmembrane protein

MacromoleculeName: unidentified transmembrane protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 1.652805 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAA

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Macromolecule #19: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL...

MacromoleculeName: (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
type: ligand / ID: 19 / Number of copies: 7 / 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 #20: 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: 20 / Number of copies: 2 / 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 #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 34 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 9 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #23: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #24: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 24 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #25: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 25 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #26: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 26 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #27: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #28: 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: 28 / Number of copies: 1 / 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 #29: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 29 / Number of copies: 2 / Formula: UNL
Molecular weightTheoretical: 294.408 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #30: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 30 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #31: heptyl 1-thio-beta-D-glucopyranoside

MacromoleculeName: heptyl 1-thio-beta-D-glucopyranoside / type: ligand / ID: 31 / Number of copies: 1 / Formula: HTG
Molecular weightTheoretical: 294.408 Da
Chemical component information

ChemComp-HTG:
heptyl 1-thio-beta-D-glucopyranoside / detergent*YM

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194738
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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