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- EMDB-37133: Cryo-EM structure of an intermediate-state complex during the pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-37133
TitleCryo-EM structure of an intermediate-state complex during the process of photosystem II repair
Map data
Sample
  • Complex: Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
    • Protein or peptide: x 18 types
  • Ligand: x 12 types
Keywordsmonomeric Photosystem II / PSII repair / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem II repair / oxygen evolving activity / 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 / chlorophyll binding ...photosystem II repair / oxygen evolving activity / 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 / 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding
Similarity search - Function
Chloroplast thylakoid lumenal protein MPH2 / : / Maintenance of Photosystem II under High light 2 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily ...Chloroplast thylakoid lumenal protein MPH2 / : / Maintenance of Photosystem II under High light 2 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / 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.
Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Uncharacterized protein / Uncharacterized protein / Maintenance of Photosystem II under High light 2 C-terminal domain-containing protein / Uncharacterized protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K / Photosystem II reaction center protein H ...Photosystem II CP47 reaction center protein / Uncharacterized protein / Uncharacterized protein / Maintenance of Photosystem II under High light 2 C-terminal domain-containing protein / Uncharacterized protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLi A / Wang Y / Liu Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925024 China
Chinese Academy of SciencesYSBR-015 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii.
Authors: Anjie Li / Tingting You / Xiaojie Pang / Yidi Wang / Lijin Tian / Xiaobo Li / Zhenfeng Liu /
Abstract: Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs ...Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.
History
DepositionAug 9, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37133.png

Downloads & links

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Map

FileDownload / File: emd_37133.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.9
Minimum - Maximum-0.9602674 - 61.421157999999998
Average (Standard dev.)0.0030603162 (±0.9954914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of an intermediate-state complex during the pro...

EntireName: Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
Components
  • Complex: Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
    • 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 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 Ycf12
    • Protein or peptide: Uncharacterized protein
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Thylakoid enriched factor 14 (TEF14)
    • Protein or peptide: Photosystem II repair factor 1 (PRF1)
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II repair factor 2 (PRF2)
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • 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: PHEOPHYTIN A
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: RRR-ALPHA-TOCOPHERYLQUINONE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: BICARBONATE ION
  • Ligand: FE (II) ION

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Supramolecule #1: Cryo-EM structure of an intermediate-state complex during the pro...

SupramoleculeName: Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: chloroplast

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Macromolecule #1: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 56.089703 KDa
SequenceString: MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV ...String:
MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV SDPYGLTGSV QPVAPSWGAD GFDPYNPGGI ASHHIAAGIL GVLAGLFHLC VRPSIRLYFG LSMGSIETVL SS SIAAVFW AAFVVAGTMW YGSAATPIEL FGPTRYQWDQ GFFQQEIQKR VQASLAEGAS LSDAWSRIPE KLAFYDYIGN NPA KGGLFR TGAMNSGDGI AVGWLGHASF KDQEGRELFV RRMPTFFETF PVLLLDKDGI VRADVPFRKA ESKYSIEQVG VSVT FYGGE LDGLTFTDPA TVKKYARKAQ LGEIFEFDRS TLQSDGVFRS SPRGWFTFGH VCFALLFFFG HIWHGARTIF RDVFA GIDD DINDQVEFGK YKKLGDTSSL REAF

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #2: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.474031 KDa
SequenceString: MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF ...String:
MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLLVPVT GLWMSAIGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ERLVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #3: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.312598 KDa
SequenceString:
MAGKPVERPF SDILTSIRYW VIHSITVPAL FIAGWLFVST GLAYDVFGTP RPNEYFTEDR QEAPLITDRF NALEQVKKLS GN

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #4: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.986013 KDa
SequenceString:
MTTKKSAEVL VYPIFTVRWL AIHGIAVPTI FFLGAITAMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #5: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.445063 KDa
SequenceString:
MATGTSKAKP SKVNSDFQEP GLVTPLGTLL RPLNSEAGKV LPGWGTTVLM AVFILLFAAF LLIILEIYNS SLILDDVSMS WETLAKVS

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #6: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.245035 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGKNLD

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #7: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 5.062142 KDa
SequenceString:
MTTLALVLAK LPEAYAPFAP IVDVLPVIPV FFILLAFVWQ AAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #8: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.431229 KDa
SequenceString:
MARPNPNKQV VELNRTSLYW GLLLIFVLAV LFSSYIFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #9: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.762433 KDa
SequenceString:
MEVNIYGLTA TALFIIIPTS FLLILYVKTA STQD

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #10: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.639438 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFRDPPRMI K

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #11: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.333058 KDa
SequenceString:
MNIELALTLV SLVLVVSAGP LVVVLLSARG GNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #12: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.894716 KDa
SequenceString:
MAAVCVSSKA VAVRPATRVA SRPAARMVVR ASAKPAQISE KAIAAGVSAA AAASLALAPI AEAAVTPSLK NFLGSLIAGA TVLGGIALA ITAVSKFDKT IR

UniProtKB: Uncharacterized protein

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.565863 KDa
SequenceString:
MTSILQVALL ALIFVSFALV VGVPVVFATP NGWTDNKGAV FSGLSLWLLL VFVVGILNSF VV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #14: Thylakoid enriched factor 14 (TEF14)

MacromoleculeName: Thylakoid enriched factor 14 (TEF14) / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.601596 KDa
SequenceString: MALMMQKVAA PVSRRGMKVV AQATPNTASR RAILGVALLP ALMYAPKALA LIPDEEDEDL VEKAKANRRA RLAQQRGVTR DFMASENLT DRRLEQELVP VQKAVYKLAK SGSQLESGDL KGAASTLSES WVGDFSTVAS TVSGSTTAGK LVEAIKSVQA A AAKGDAAG ...String:
MALMMQKVAA PVSRRGMKVV AQATPNTASR RAILGVALLP ALMYAPKALA LIPDEEDEDL VEKAKANRRA RLAQQRGVTR DFMASENLT DRRLEQELVP VQKAVYKLAK SGSQLESGDL KGAASTLSES WVGDFSTVAS TVSGSTTAGK LVEAIKSVQA A AAKGDAAG SKRAYVSLVS DLQSWADASG LATSLKGL

UniProtKB: Maintenance of Photosystem II under High light 2 C-terminal domain-containing protein

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Macromolecule #15: Photosystem II repair factor 1 (PRF1)

MacromoleculeName: Photosystem II repair factor 1 (PRF1) / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 13.340966 KDa
SequenceString:
MLSNARAAVS KVHTSSAAVA PARPARVSHI VRASDKKLDE RGVIAKDNSG RQNIFPTSSK AYYSSPTSSA VASSGLGGQQ GLGVLAAAF AIVALATAGV VLKQGDETLA QVNNAYQGDS LTVISSRIAE SL

UniProtKB: Uncharacterized protein

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Macromolecule #16: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 50.680738 KDa
SequenceString: METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM ...String:
METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM YFGGVYDTWA PGGGDVRVIT NPTTNAAVIF GYLVKSPFGG DGWICSVDNM EDIIGGHIWI GTLEILGGIW HI YTTPWPW ARRAFVWSGE AYLSYSLGAI GVMGFIACCM SWFNNTAYPS EFYGPTGPEA SQSQAFTFLV RDQRLGANVA SAQ GPTGLG KYLMRSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KLKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINAV NFVSPRSWLA CSHFCLGFFF FIGHLWHAGR ARAAAAGFEK GIDRFDEPVL SMRPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #17: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.06634 KDa
SequenceString: MTAILERREN SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL V YPIGQGSF ...String:
MTAILERREN SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WPVIGIWFTA LGLSTMAFNL NGFNFNQSVV DSQGRVLNTW ADI INRANL GMEVMHERNA HNFPLDLAST NSSSNN

UniProtKB: Photosystem II protein D1

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Macromolecule #18: Photosystem II repair factor 2 (PRF2)

MacromoleculeName: Photosystem II repair factor 2 (PRF2) / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 12.002007 KDa
SequenceString:
MAALRCSVAT RAAVPARRSS VVVRASTEQT TKRAMLGLLA GAVAGALLVA PAEAIRIPSH EFTGGMVKGG GSSPKSPTAA SMESYTLEG TKKQGVSLKT KKKLLAKVRE NAQKSASS

UniProtKB: Uncharacterized protein

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 20 / Number of copies: 10 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #21: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 21 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 10 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #23: 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: 23 / Number of copies: 1 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE

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Macromolecule #24: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 24 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #25: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 25 / 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 #26: RRR-ALPHA-TOCOPHERYLQUINONE

MacromoleculeName: RRR-ALPHA-TOCOPHERYLQUINONE / type: ligand / ID: 26 / Number of copies: 1 / Formula: VTQ
Molecular weightTheoretical: 446.706 Da
Chemical component information

ChemComp-VTQ:
RRR-ALPHA-TOCOPHERYLQUINONE

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #28: 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: 28 / Number of copies: 1 / 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 #29: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 29 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Macromolecule #30: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 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: 6.5
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 510932
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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