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- EMDB-60830: Cryo-EM structure of a TEF30-associated intermediate C2S-type PSI... -

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Basic information

Entry
Database: EMDB / ID: EMD-60830
TitleCryo-EM structure of a TEF30-associated intermediate C2S-type PSII-LHCII supercomplex from Chlamydomonas reinhardtii
Map data
Sample
  • Complex: TEF30-associated C2S-type PSII-LHCII supercomplex
    • Protein or peptide: x 22 types
  • Protein or peptide: x 1 types
  • Ligand: x 16 types
Keywordsphotosystem II / PSII repair / PSII assembly / PSII intermediate / TEF30 / C2S / supercomplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / 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 ...thylakoid light-harvesting complex / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / 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 I / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / : / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / 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 D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 1, chloroplastic / 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 D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 1, chloroplastic / 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 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein CP29 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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
DepositionJul 16, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60830.png

Downloads & links

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Map

FileDownload / File: emd_60830.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.8
Minimum - Maximum-20.689045 - 39.153754999999997
Average (Standard dev.)0.008478108 (±1.163341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TEF30-associated C2S-type PSII-LHCII supercomplex

EntireName: TEF30-associated C2S-type PSII-LHCII supercomplex
Components
  • Complex: TEF30-associated C2S-type PSII-LHCII supercomplex
    • 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: Chlorophyll a-b binding protein, chloroplastic
    • 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: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Oxygen-evolving enhancer protein 1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: Chloroplast photosystem II subunit X
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Chlorophyll a-b binding protein CP29
  • Protein or peptide: PDZ domain-containing protein
  • 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: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Supramolecule #1: TEF30-associated C2S-type PSII-LHCII supercomplex

SupramoleculeName: TEF30-associated C2S-type PSII-LHCII supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#23
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: PDZ domain-containing protein

MacromoleculeName: PDZ domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 18.299564 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AAEKQWKKER AGGNYGAGTK EIQARNYVQR KENERKRREM FDDALAKFKE NDIQGALVEF ENIIAMEPRN FVGDNFSRNT PIYKVTQYN IACCYSMLDQ VEEAIKSLDA AMLSGFDNYD QIRRDKNLSK ARANPKFQAV LDKYDEPVVN WNAVKATFGA

UniProtKB: PDZ domain-containing protein

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Macromolecule #2: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 37.172312 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 AHNFPLDLA

UniProtKB: Photosystem II protein D1

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Macromolecule #3: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 53.051438 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 I

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #4: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 49.416305 KDa
SequenceString: GRDQETTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE IIDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIMLGLGAW LLVWKAMYFG G VYDTWAPG ...String:
GRDQETTGFA WWSGNARLIN LSGKLLGAHV AHAGLIVFWA GAMNLFEVSH FVPEKPMYEQ GLILLPHIAT LGYGVGPGGE IIDTFPYFV SGVLHLISSA VLGFGGVYHS LIGPETLEES YPFFGYVWKD KNKMTNILGY HLIMLGLGAW LLVWKAMYFG G VYDTWAPG GGDVRVITNP TTNAAVIFGY LVKSPFGGDG WICSVDNMED IIGGHIWIGT LEILGGIWHI YTTPWPWARR AF VWSGEAY LSYSLGAIGV MGFIACCMSW FNNTAYPSEF YGPTGPEASQ SQAFTFLVRD QRLGANVASA QGPTGLGKYL MRS PTGEII FGGETMRFWD FRGPWLEPLR GPNGLDLNKL KNDIQPWQER RAAEYMTHAP LGSLNSVGGV ATEINAVNFV SPRS WLACS HFCLGFFFFI GHLWHAGRAR AAAAGFEKGI DRFDEPVLSM RPLD

UniProtKB: Photosystem II CP43 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: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.342836 KDa
SequenceString: TIAIGTYQEK RTWFDDADDW LRQDRFVFVG WSGLLLFPCA YFALGGWLTG TTFVTSWYTH GLATSYLEGC NFLTAAVSTP ANSMAHSLL FVWGPEAQGD FTRWCQLGGL WAFVALHGAF GLIGFMLRQF EIARSVNLRP YNAIAFSAPI AVFVSVFLIY P LGQSGWFF ...String:
TIAIGTYQEK RTWFDDADDW LRQDRFVFVG WSGLLLFPCA YFALGGWLTG TTFVTSWYTH GLATSYLEGC NFLTAAVSTP ANSMAHSLL FVWGPEAQGD FTRWCQLGGL WAFVALHGAF GLIGFMLRQF EIARSVNLRP YNAIAFSAPI AVFVSVFLIY P LGQSGWFF APSFGVAAIF RFILFFQGFH NWTLNPFHMM GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ AE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLLVPVTG LWMSAIGVVG LALNLRAYDF VSQEIRAAED PEFETFYTKN ILL NEGIRA WMAAQDQPHE RLVFPEEVLP RGNAL

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: 2 / 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 #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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 #8: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.56159 KDa
SequenceString: EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKNGIPFG EAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR ANGGPLGEGL DPLHPGGAFD PLGLADDPDT F AELKVKEI ...String:
EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKNGIPFG EAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR ANGGPLGEGL DPLHPGGAFD PLGLADDPDT F AELKVKEI KNGRLAMFSM FGFFVQAIVT GKGPIQNLDD HLANPTAVNA FAYATKFTPS A

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #9: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 7.504862 KDa
SequenceString:
QEPGLVTPLG TLLRPLNSEA GKVLPGWGTT VLMAVFILLF AAFLLIILEI YNSSLILDDV SMSWETLAK

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #10: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.01679 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGKN

UniProtKB: Photosystem II reaction center protein I

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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: 2 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.300033 KDa
SequenceString:
ARPNPNKQVV ELNRTSLYWG LLLIFVLAVL FSSYIFN

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.387036 KDa
SequenceString:
VNIYGLTATA LFIIIPTSFL LILYVKTAST Q

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.6486 KDa
SequenceString: EFYGPNRAKW LGPYSENATP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKSGTQFG EAVWFKAGA QIFSEGGLDY LGNPSLVHAQ NIVATLAVQV ILMGLVEGYR VNGGPAGEGL DPLYPGESFD PLGLADDPDT F AELKVKEI ...String:
EFYGPNRAKW LGPYSENATP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWAM LGALGCITPE LLAKSGTQFG EAVWFKAGA QIFSEGGLDY LGNPSLVHAQ NIVATLAVQV ILMGLVEGYR VNGGPAGEGL DPLYPGESFD PLGLADDPDT F AELKVKEI KNGRLAMFSM FGFFVQAIVT GKGPIQNLDD HLSNPTVNNA FAFATKFTPS A

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #15: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.704027 KDa
SequenceString: LTFDEIQGLT YLQVKGSGIA NTCPVLESGT TNLKELKAGS YKLENFCIEP TSFTVKEESQ FKGGETEFVK TKLMTRLTYT LDAMSGSFK VGSDGSAELK EDDGIDYAAT TVQLPGGERV AFLFTIKQFD GKGTLDGIKG DFLVPSYRGS SFLDPKGRGG S TGYDNAVA ...String:
LTFDEIQGLT YLQVKGSGIA NTCPVLESGT TNLKELKAGS YKLENFCIEP TSFTVKEESQ FKGGETEFVK TKLMTRLTYT LDAMSGSFK VGSDGSAELK EDDGIDYAAT TVQLPGGERV AFLFTIKQFD GKGTLDGIKG DFLVPSYRGS SFLDPKGRGG S TGYDNAVA LPARADAEEL LKENVKITKA LKGSAVFSVA KVDPVTGEIA GVFESIQPSD TDLGAKPPKD IKVTGLWYAQ LK

UniProtKB: Oxygen-evolving enhancer protein 1, chloroplastic

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Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 26.767156 KDa
SequenceString: KATRGWLGGQ GGAADLDKWY GPDRKLFLPS GLYDRSEIPE YLNGELAGDY GYDPLGLGKD PETVAKYREN ELLHARWAML AAAGILIPE GLQANGANIK GGTWFETGAE MLNGGTLNYF AVPWGIVSNP LPLFAVIAVE VGLMGAVEFY RRNGTGPAGY S PGIGKFDS ...String:
KATRGWLGGQ GGAADLDKWY GPDRKLFLPS GLYDRSEIPE YLNGELAGDY GYDPLGLGKD PETVAKYREN ELLHARWAML AAAGILIPE GLQANGANIK GGTWFETGAE MLNGGTLNYF AVPWGIVSNP LPLFAVIAVE VGLMGAVEFY RRNGTGPAGY S PGIGKFDS SVFDGLDPLY PGGPFDPLGL ADDPEVLQEL KVKEIKNGRL AMVSVLGFAV QSYVTGEGPY ANWTKHVADP FG YNLLTVL GAE

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #17: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.510259 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFRDPPRMI

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #18: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / 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 #19: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.158926 KDa
SequenceString:
LVDERMNGDG TGRPFGVNDP VLGWVLLGVF GTMWAIWFIG QKDLGDFEDA DDGLKL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

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Macromolecule #20: Chloroplast photosystem II subunit X

MacromoleculeName: Chloroplast photosystem II subunit X / type: protein_or_peptide / ID: 20 / Number of copies: 2 / 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 #21: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.808879 KDa
SequenceString: PDSFWYGPER PLFLGAFTGE PPSYLTGEFP GDYGWDTAGL SADPETFKRY RELELIHARW AMLGALGCIF PELLGSYGVP FGEAVWFKA GAQIFQEGGL DYLGNPNLVH AQSILAILGT QVLLMGAIEG YRVNGGPLGE GLDKLYPGGS FDPLGLADDP D TFAELKVK ...String:
PDSFWYGPER PLFLGAFTGE PPSYLTGEFP GDYGWDTAGL SADPETFKRY RELELIHARW AMLGALGCIF PELLGSYGVP FGEAVWFKA GAQIFQEGGL DYLGNPNLVH AQSILAILGT QVLLMGAIEG YRVNGGPLGE GLDKLYPGGS FDPLGLADDP D TFAELKVK EIKNGRLAMF SMFGFFVQAI VTGKGPLQNL SDHLANPGTN NAFAYATKFT PQ

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #22: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 22 / Number of copies: 2 / 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 #23: Chlorophyll a-b binding protein CP29

MacromoleculeName: Chlorophyll a-b binding protein CP29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 21.906639 KDa
SequenceString: RPEWLDGSLP GDRGFDPLGL SKPSEFVVIG VDENDQNAAK NNKGSVEAIV QATPDEVSSE NRLAPYSEVF GLARFRECEL IHGRWAMLA CLGALVAEAT TGVSWVEAGK VELDGASYAG LSLPFSITQL IWIEVILVGG AEFYRNSETN PEKRCYPGGV F DPLKLASE ...String:
RPEWLDGSLP GDRGFDPLGL SKPSEFVVIG VDENDQNAAK NNKGSVEAIV QATPDEVSSE NRLAPYSEVF GLARFRECEL IHGRWAMLA CLGALVAEAT TGVSWVEAGK VELDGASYAG LSLPFSITQL IWIEVILVGG AEFYRNSETN PEKRCYPGGV F DPLKLASE DEERAFRLKT AEIKHARLAM VSFFGYGVQA LST

UniProtKB: Chlorophyll a-b binding protein CP29

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Macromolecule #24: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 24 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 109 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 26 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #27: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 27 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: 3 / 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 15 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / 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 #32: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 32 / Number of copies: 4 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #33: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #34: 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: 34 / Number of copies: 2 / 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 #35: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 35 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #36: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 36 / Number of copies: 25 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #37: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 37 / Number of copies: 8 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #38: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 38 / Number of copies: 5 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Macromolecule #39: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 39 / Number of copies: 4 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Experimental details

-
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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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