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- EMDB-60605: Cryo-EM structure of an TEF30-associated intermediate PSII core c... -

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Basic information

Entry
Database: EMDB / ID: EMD-60605
TitleCryo-EM structure of an TEF30-associated intermediate PSII core complex from Chlamydomonas reinhardtii
Map data
Sample
  • Complex: TEF30-associated PSII core complex
    • Protein or peptide: x 17 types
  • Ligand: x 13 types
Keywordsphotosystem II / PSII repair / PSII assembly / PSII intermediate / TEF30 / PHOTOSYNTHESIS
Function / homology
Function and homology information


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 / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II ...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 / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / : / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / 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 ...Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / 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 PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / 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. / PDZ domain / PDZ domain profile. / PDZ domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PDZ domain-containing protein / Uncharacterized protein / Photosystem II reaction center protein J / 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 CP47 reaction center protein ...PDZ domain-containing protein / Uncharacterized protein / Photosystem II reaction center protein J / 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 CP47 reaction center protein / 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: 2.98 Å
AuthorsWang Y / Wang C / Li A / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Plants / Year: 2025
Title: Roles of multiple TEF30-associated intermediate complexes in the repair and reassembly of photosystem II in Chlamydomonas reinhardtii.
Authors: Yidi Wang / Chenxi Wang / Anjie Li / Zhenfeng Liu /
Abstract: During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a ...During oxygenic photosynthesis, photosystem II (PSII) uses light energy for oxidizing water and reducing plastoquinone. It is susceptible to photodamage, and the damaged PSII is repaired through a sophisticated biological process assisted by numerous auxiliary proteins. Here we report the cryogenic electron microscopy structures of four PSII-repair complexes from Chlamydomonas reinhardtii associated with the Thylakoid Enriched Fraction 30 (TEF30, an orthologue of plant MET1) protein-namely, a TEF30-PSII core monomer (TEF30-C), two types of TEF30-PSII core dimers (types I and II, TEF30-C-I and TEF30-C-II) and a TEF30-CS-type PSII-LHCII supercomplex (TEF30-CS; S, strongly associated light-harvesting complex II trimer). TEF30 mediates the assembly of CP43 with the RC47 module by clamping on the stromal surfaces and prevents the premature association of peripheral antennae with PSII-C. In the transition from TEF30-C-I to TEF30-C-II, TEF30-CS and mature CS, one PSII core slides along the dimerization interface against the adjacent one by 22-35 Å, generating a zigzagged surface for accommodating the peripheral antennae. These results suggest that the PSII repair process undergoes multiple TEF30-mediated intermediate states to form intact PSII-LHCII supercomplexes.
History
DepositionJun 21, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60605.png

Downloads & links

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Map

FileDownload / File: emd_60605.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum-0.88296056 - 1.3966858
Average (Standard dev.)0.0022165054 (±0.044610124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60605_half_map_1.map
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Half map: #1

Fileemd_60605_half_map_2.map
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Sample components

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Entire : TEF30-associated PSII core complex

EntireName: TEF30-associated PSII core complex
Components
  • Complex: TEF30-associated PSII core complex
    • 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: PDZ domain-containing protein
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Chloroplast photosystem II subunit X
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: BICARBONATE 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: water

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Supramolecule #1: TEF30-associated PSII core complex

SupramoleculeName: TEF30-associated PSII core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 36.192223 KDa
SequenceString: NSSLWARFCE WITSTENRLY IGWFGVIMIP CLLTATSVFI IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVIPTSNAI GLHFYPIWE AASLDEWLYN GGPYQLIVCH FLLGVYCYMG REWELSFRLG MRPWIAVAYS APVAAASAVF LVYPIGQGSF S DGMPLGIS ...String:
NSSLWARFCE WITSTENRLY IGWFGVIMIP CLLTATSVFI IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVIPTSNAI GLHFYPIWE AASLDEWLYN GGPYQLIVCH FLLGVYCYMG REWELSFRLG MRPWIAVAYS APVAAASAVF LVYPIGQGSF S DGMPLGIS GTFNFMIVFQ AEHNILMHPF HMLGVAGVFG GSLFSAMHGS LVTSSLIRET TENESANEGY RFGQEEETYN IV AAHGYFG RLIFQYASFN NSRSLHFFLA AWPVIGIWFT ALGLSTMAFN LNGFNFNQSV VDSQGRVLNT WADIINRANL GME VMHERN

UniProtKB: Photosystem II protein D1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 52.938281 KDa
SequenceString: GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS ...String:
GLPWYRVHTV VINDPGRLIS VHLMHTALVS GWAGSMALFE ISVFDPSDPV LNPMWRQGMF VLPFMTRLGI TQSWGGWTIS GETATNPGI WSYEGVAAAH IILSGALFLA SVWHWTYWDL ELFRDPRTGK TALDLPKIFG IHLFLSGLLC FGFGAFHVTG V FGPGIWVS DPYGLTGRVQ PVAPSWGADG FDPYNPGGIA SHHIAAGILG VLAGLFHLCV RPSIRLYFGL SMGSIETVLS SS IAAVFWA AFVVAGTMWY GSAATPIELF GPTRYQWDQG FFQQEIQKRV QASLAEGASL SDAWSRIPEK LAFYDYIGNN PAK GGLFRT GAMNSGDGIA VGWLGHASFK DQEGRELFVR RMPTFFETFP VLLLDKDGIV RADVPFRKAE SKYSIEQVGV SVTF YGGEL DGLTFTDPAT VKKYARKAQL GEIFEFDRST LQSDGVFRSS PRGWFTFGHV CFALLFFFGH IWHGARTIFR DVFAG

UniProtKB: Photosystem II CP47 reaction center protein

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.473355 KDa
SequenceString: GGRDQETTGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVS HFVPEKPMYE QGLILLPHIA TLGYGVGPGG EIIDTFPYF VSGVLHLISS AVLGFGGVYH SLIGPETLEE SYPFFGYVWK DKNKMTNILG YHLIMLGLGA WLLVWKAMYF G GVYDTWAP ...String:
GGRDQETTGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMNLFEVS HFVPEKPMYE QGLILLPHIA TLGYGVGPGG EIIDTFPYF VSGVLHLISS AVLGFGGVYH SLIGPETLEE SYPFFGYVWK DKNKMTNILG YHLIMLGLGA WLLVWKAMYF G GVYDTWAP GGGDVRVITN PTTNAAVIFG YLVKSPFGGD GWICSVDNME DIIGGHIWIG TLEILGGIWH IYTTPWPWAR RA FVWSGEA YLSYSLGAIG VMGFIACCMS WFNNTAYPSE FYGPTGPEAS QSQAFTFLVR DQRLGANVAS AQGPTGLGKY LMR SPTGEI IFGGETMRFW DFRGPWLEPL RGPNGLDLNK LKNDIQPWQE RRAAEYMTHA PLGSLNSVGG VATEINAVNF VSPR SWLAC SHFCLGFFFF IGHLWHAGRA RAAAAGFEKG IDRFDEPVLS MRPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.128578 KDa
SequenceString: AIGTYQEKRT WFDDADDWLR QDRFVFVGWS GLLLFPCAYF ALGGWLTGTT FVTSWYTHGL ATSYLEGCNF LTAAVSTPAN SMAHSLLFV WGPEAQGDFT RWCQLGGLWA FVALHGAFGL IGFMLRQFEI ARSVNLRPYN AIAFSAPIAV FVSVFLIYPL G QSGWFFAP ...String:
AIGTYQEKRT WFDDADDWLR QDRFVFVGWS GLLLFPCAYF ALGGWLTGTT FVTSWYTHGL ATSYLEGCNF LTAAVSTPAN SMAHSLLFV WGPEAQGDFT RWCQLGGLWA FVALHGAFGL IGFMLRQFEI ARSVNLRPYN AIAFSAPIAV FVSVFLIYPL G QSGWFFAP SFGVAAIFRF ILFFQGFHNW TLNPFHMMGV AGVLGAALLC AIHGATVENT LFEDGDGANT FRAFNPTQAE ET YSMVTAN RFWSQIFGVA FSNKRWLHFF MLLVPVTGLW MSAIGVVGLA LNLRAYDFVS QEIRAAEDPE FETFYTKNIL LNE GIRAWM AAQDQPHERL VFPEEVLPRG NAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.598734 KDa
SequenceString:
RPFSDILTSI RYWVIHSITV PALFIAGWLF VSTGLAYDVF GTPRPNEYFT EDRQEAPLIT DRFNALEQVK KLSGN

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.535273 KDa
SequenceString:
IFTVRWLAIH GIAVPTIFFL GAITAMQFIQ R

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: PDZ domain-containing protein

MacromoleculeName: PDZ domain-containing protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 29.196828 KDa
SequenceString: SEAEYIELDL PKPLGFKFAR GNDGGAYIIE VNPKAGNIDA RVQPGDKIVE ISASFGSEVW KAENFGQIMY AIRTRSGTVY MKLKKNYGD LSALEEEGLD AAEKQWKKER AGGNYGAGTK EIQARNYVQR KENERKRREM FDDALAKFKE NDIQGALVEF E NIIAMEPR ...String:
SEAEYIELDL PKPLGFKFAR GNDGGAYIIE VNPKAGNIDA RVQPGDKIVE ISASFGSEVW KAENFGQIMY AIRTRSGTVY MKLKKNYGD LSALEEEGLD AAEKQWKKER AGGNYGAGTK EIQARNYVQR KENERKRREM FDDALAKFKE NDIQGALVEF E NIIAMEPR NFVGDNFSRN TPIYKVTQYN IACCYSMLDQ VEEAIKSLDA AMLSGFDNYD QIRRDKNLSK ARANPKFQAV LD KYDEPVV NWNAVKATFG A

UniProtKB: PDZ domain-containing protein

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 7.652035 KDa
SequenceString:
FQEPGLVTPL GTLLRPLNSE AGKVLPGWGT TVLMAVFILL FAAFLLIILE IYNSSLILDD VSMSWETLAK

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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.902687 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGK

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #10: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.270858 KDa
SequenceString:
IPLWLVGTVV GTLAIGLLAV FFYGSYVGLG SS

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #11: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.147979 KDa
SequenceString:
KLPEAYAPFA PIVDVLPVIP VFFILLAFVW QAAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #12: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.071762 KDa
SequenceString:
PNPNKQVVEL NRTSLYWGLL LIFVLAVLFS SYIFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #13: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 2.971595 KDa
SequenceString:
NIYGLTATAL FIIIPTSFLL ILYVKTA

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #14: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 2.799394 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFR

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #15: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.201863 KDa
SequenceString:
NIELALTLVS LVLVVSAGPL VVVLLSARGG NL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #16: Chloroplast photosystem II subunit X

MacromoleculeName: Chloroplast photosystem II subunit X / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.05664 KDa
SequenceString:
AVTPSLKNFL GSLIAGATVL GGIALAITAV SK

UniProtKB: Uncharacterized protein

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Macromolecule #17: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.466732 KDa
SequenceString:
MTSILQVALL ALIFVSFALV VGVPVVFATP NGWTDNKGAV FSGLSLWLLL VFVVGILNSF V

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #18: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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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: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 20 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 10 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #22: 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: 22 / 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 #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 23 / Number of copies: 5 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 25 / 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 #26: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 26 / Number of copies: 1 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #27: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #28: 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: 28 / 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 #29: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 29 / 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 #30: water

MacromoleculeName: water / type: ligand / ID: 30 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kac

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45968
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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