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- EMDB-65026: PSI-LHCI of Euglena gracilis strain Z -

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Basic information

Entry
Database: EMDB / ID: EMD-65026
TitlePSI-LHCI of Euglena gracilis strain Z
Map data
Sample
  • Complex: PSI-LHCI
    • Protein or peptide: x 19 types
  • Ligand: x 10 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chloroplast light-harvesting complex I protein / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsKato K / Nakajima Y / Shen JR / Nagao R
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K14211, JP22H04916, and JP23H02423 Japan
CitationJournal: To Be Published
Title: Structure of a divergent photosystem I supercomplex from Euglena gracilis outside green and red lineages
Authors: Kato K / Nakajima Y / Sakamoto R / Kumazawa M / Ifuku K / Shen JR / Takabayashi A / Nagao R
History
DepositionJun 11, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65026.png

Downloads & links

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Map

FileDownload / File: emd_65026.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 288 pix.
= 216.576 Å		0.75 Å/pix.
x 288 pix.
= 216.576 Å		0.75 Å/pix.
x 288 pix.
= 216.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.03249011 - 0.075970955
Average (Standard dev.)0.0005085148 (±0.0036442357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 216.57599 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: This map was used for model building.

Fileemd_65026_additional_1.map
AnnotationThis map was used for model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65026_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65026_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PSI-LHCI

EntireName: PSI-LHCI
Components
  • Complex: PSI-LHCI
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: LHCI-1
    • Protein or peptide: LHCI-2
    • Protein or peptide: LHCI-3
    • Protein or peptide: LHCI-4
    • Protein or peptide: Chloroplast light-harvesting complex I protein
    • Protein or peptide: LHCI-6
    • Protein or peptide: LHCI-7
    • Protein or peptide: LHCI-8
    • Protein or peptide: LHCI-9
    • Protein or peptide: LHCI-10
    • Protein or peptide: LHCI-11
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: UNKNOWN LIGAND
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: water

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Supramolecule #1: PSI-LHCI

SupramoleculeName: PSI-LHCI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 85.183594 KDa
SequenceString: VYDNLIENYM TITPPEQQVK RVRVAFVSNP VETSFEKWSR PGHFSRLLSK GPNTTTWIWN LHADAHDFDN HTTDLEDISR KVFSAHFGQ LAIIEIWLSG MFFHGARFSN YEAWLLDPIH VKPSAQIVWP IVGQEILNGD VGGNFQGIQI TSGLFQLWRS C GITSEFQL ...String:
VYDNLIENYM TITPPEQQVK RVRVAFVSNP VETSFEKWSR PGHFSRLLSK GPNTTTWIWN LHADAHDFDN HTTDLEDISR KVFSAHFGQ LAIIEIWLSG MFFHGARFSN YEAWLLDPIH VKPSAQIVWP IVGQEILNGD VGGNFQGIQI TSGLFQLWRS C GITSEFQL YITALTGLIF SAVLFFAGWF HYHKAAPKLE WFQNVESMLN HHLSGLLGLG CLSWAGHQIH VSLPINKLLD SG VNPAELP LPHDFILDKS LISQLYPSFS KGLAPFFTFH WSEYSDFLTF RGGLNNVTGG LWLTDVAHHH LALAVLFILA GHM YKTNWK IGHDIKGLLE SHTGPFTGQG HKGLYEIFTN SWHAQLSLNL AMMGSLSIIV AQHMYSMPPY PYIAIDYGTE LSLF THHYW IGGFCIVGAA AHAAIFMVRD YDPALNFNNL LDRVLLHRDA IISHLNWVCI FLGLHSFGLY IHNDTLSALG RPQDM FSDS AIQLQPVFAQ WIQNTHYLAP TLTAFNLVSP TTPVWGGDVV SISGKVAMMP IKLGTADFLV HHIHAFTIHV TVLILL KGV LFSRSSRLIP DKASLGFRFP CDGPGRGGTC QVSAWDHVFL GLFWMYNSIS VAIFHFSWKM QSDVWGTVLA NKVSHIT GG NFSQGSLTIN GWLRDFLWAQ SSQVIQSYGS PLSAYGLMFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAP N IQPRALSITQ GRAVGVAHYL LGGIATTWSF FLARIISVG

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 82.780266 KDa
SequenceString: MATKFPKFSQ GLAQDPTTRR IWFGIATSHD FESHDGMTEN NLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEQWIKD PLHIRPIAH AISDPHFGQP AIEAFTRSQF PGPVNIAYSG VYQWWYTIGL RTNVDLYNGS MFLLFIATLA LFAGWLHLEP K YSPKVSWF ...String:
MATKFPKFSQ GLAQDPTTRR IWFGIATSHD FESHDGMTEN NLYQKIFASH FGQLAIIFLW TSGNLFHVAW QGNFEQWIKD PLHIRPIAH AISDPHFGQP AIEAFTRSQF PGPVNIAYSG VYQWWYTIGL RTNVDLYNGS MFLLFIATLA LFAGWLHLEP K YSPKVSWF KDAESRLNHH LSALFGLSSL AWSGHLIHVA IPESRGIHVR WDNFLSQLPH PSGLEPFFKG NWSLYSENPD SL THVFGTA SGAGTAVLTF LGGFHPETKS LWLTDIAHHH LAIAVLFIVA GHMYRTNFAI GHRIDDILNA HKAPSGKLGL GHF GLYETI NNSLHFQLGL ALASLGVITS LVAQHMYSLS PYAFLIQDRT TMAALYTHHQ YIAGFIMTGA FAHGAIFFIR DFDE EKNKG NVLSRILDHK EAIISHLSWV TLFLGFHTLG LYVHNDVMQA FGTPEKQILI EPVFAQWIQS AHGKNIYELN ILLSS DSSN AFSASQAIWL PGWLNGINDK STSLFLQIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS RLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWTTFY WHWKHITLWQ GNVGQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LAVWGWMFLF GHLVWATGFM FLISWRGYWQ ELIETLVWAH ERTPITNVFK WTDKPVALSI VQARLVGLAH FSVGYVFT Y AAFLIASTSA KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 8.784116 KDa
SequenceString:
MSHSVKIYNT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SSPRTEDCVG CKRCESACPT DFLSVRVYLG SETSRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 76.196211 KDa
SequenceString: LAAGALFGLA LSPSVASNYA APSAVRASTT ISAVRPVVFT GSYVRGVQTG RTTVVEATPN QEVETLASAN NLWVTAAAAG LAFSAASLV LALLRKPRSE ETYSMLAEAA EVGKAPWTAP KLEDALKNEK ARQKAEALST QLPVFWDLRD ALGEVPKSKF P EVFARYKG ...String:
LAAGALFGLA LSPSVASNYA APSAVRASTT ISAVRPVVFT GSYVRGVQTG RTTVVEATPN QEVETLASAN NLWVTAAAAG LAFSAASLV LALLRKPRSE ETYSMLAEAA EVGKAPWTAP KLEDALKNEK ARQKAEALST QLPVFWDLRD ALGEVPKSKF P EVFARYKG STGTLLSAAK TEEYYAITWT SPKTQIYELP TGGAAEMDEG LNIMYFARKE QCLALGAQLR TKFKPRIESF AI YRVFPNG ETQYLHPKDG VFPEKVNQGR TKANHNPRSI GENKEPASVK FTGTTPKDVQ TEGAVAMFAE TGEKAAKPAW TVP DLADAL KNTSAVAKAK GIATQLPTFW ELRDALSEVP KSKFPEVFAS YKGSTGTLLS AAEKEEKYVI TWTSPKKQIF ELPT GGAAE MEEGENIFFF ARKEQCLALG AQLRTAFKPR IENFQIFRVF PNGEVQYLHP KDGVFPEKVN QGRTKANHNP RSIGE NAEP ASVKFTGTTP KDVQTEGAVA MFAETGEKAA KPAWTVPNLS DALKNTAAVA KAKEIATQLP TFWELRDALS EVPKSK FPE VFASYKGSTG TLLAAAEKEE KYVITWTSPK KQIFELPTGG AAEMEEGENI FYFARKEQCL ALGAQLRTAF KPRIENF QI FRVFPNGEVQ YLHPKDGVFP EKVNAGRQQA NHNARSIGEN VEPASVKFSG STPKDL

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 17.927295 KDa
SequenceString:
ECLFFFGQIT MAFNNAMADP WFKFTAVSSA TLMAIGCALM AIAELTAPQQ QALYAAPAVQ TRMITRLADD AAARVADRTQ FIEEYKERR AEAPATPKAK AGPARGSTVK VTRPESYWYN QYGKVISVDE SGAIRYPVVV RFEKENYQGV TTNNFALDEL E Y

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 35.240191 KDa
SequenceString: QNLESKQLSI FFRAEHKMYR CNYQNLESKQ WSMTAVLGVT ALLSVSVGAT AGFIASQPST TSLYAPASTT TSISSVAAIP VSQAAARAP VQAVPVSEAQ SVEQSIYTEA PQASFNWAPV AALIALPTAI AAFLLRRSEN EVKLATAGVA ASAVLASGAM T AMPANATE ...String:
QNLESKQLSI FFRAEHKMYR CNYQNLESKQ WSMTAVLGVT ALLSVSVGAT AGFIASQPST TSLYAPASTT TSISSVAAIP VSQAAARAP VQAVPVSEAQ SVEQSIYTEA PQASFNWAPV AALIALPTAI AAFLLRRSEN EVKLATAGVA ASAVLASGAM T AMPANATE AILGLTPCAE SAKFQKVLTK EVKALEKREK LYEPGSAPFQ ALEATKAKTQ ARFAKYAESG LLCGADGLPH LI SDPGLAV KYGHAGETLI PTIGFLYVAG YIGTAGRTYL QEISTRQKPT QSEIIIDVPL ATSIAFKSWD WPNKAVKELA SGT LLEDAK NVPVSRR

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Macromolecule #7: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 4.298092 KDa
SequenceString:
MKYFTTYLST APVVAVLWFT LTASLLIEIN RFFPDIL

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #8: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 3.445077 KDa
SequenceString:
MEITTNQVYI ALLASLIPAF FAFKLGKSLN Q

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #9: LHCI-1

MacromoleculeName: LHCI-1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 52.475848 KDa
SequenceString: LVGFVAAQTT SLHAPVVVRP VVQASTLAVP AARAGRANVL LRAGTESQIV PKNGFATKVN VAFVPLACGV GALAALVATL VHKKEQPLA MLATSGEKRP TWFPGAEAPA WLTGEFPGDR GFDPCGLARD PVDFAKFRDS EVFHGRWAML GLVGCLVPEV F GNLGIAQL ...String:
LVGFVAAQTT SLHAPVVVRP VVQASTLAVP AARAGRANVL LRAGTESQIV PKNGFATKVN VAFVPLACGV GALAALVATL VHKKEQPLA MLATSGEKRP TWFPGAEAPA WLTGEFPGDR GFDPCGLARD PVDFAKFRDS EVFHGRWAML GLVGCLVPEV F GNLGIAQL PAWYDAATVA NTSNLDYLGN PNLVHASNVS FIALSTLLLM GPVEAWRWNG ALASEAKSAE RTTYPGGPFD PL KLGASPE LKLKEIKNGR LAMVGMFGFW AQSYVTGEGP LANLAAHLAD PAHNNLLNTV AMFAASGEKR PTWFPGAEAP AWL TGEYPG DRGFDPFGLA KDPEDFAKNR DSEVYHGRWA MLGLVGCLVP EVFGNLGIAQ LPAWYEAGAV ANTGSLDYLG NPNL VHASN VPLIFFTTLL LFLPIEAWRW NGQIAPDAKS KEWTTYPGGP FDPLKLGASP ELKLKEIKNG RLAMVGMFGF WAQSY VTGE GPLANLAA

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Macromolecule #10: LHCI-2

MacromoleculeName: LHCI-2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 65.361496 KDa
SequenceString: IFFRHSLLSS THFKMPNNAD AMKFGLAAGA AMGVIVYVLA GTASSTSLAA THVNIQQAPA VIPRMASVPS AYTIATNPIG ASARVVDAN YESTDYLTLP ATEKSTMGSL LMIAAAGVAA AVAFVWKSVP RQQDSVINVP LLPVSVATMA TSGKKSKAPA A DNLSQWYG ...String:
IFFRHSLLSS THFKMPNNAD AMKFGLAAGA AMGVIVYVLA GTASSTSLAA THVNIQQAPA VIPRMASVPS AYTIATNPIG ASARVVDAN YESTDYLTLP ATEKSTMGSL LMIAAAGVAA AVAFVWKSVP RQQDSVINVP LLPVSVATMA TSGKKSKAPA A DNLSQWYG PDRAKWLGPL TGQVPAYLTG ELPGDYGWDT AGLGADPVTL ARYREAEVIH ARWAMLGALG VVTPELLAGN GV PFGEGAV WYKAGAQIFS ADGLNYLGNP SLIHAQSVVL TFLSTLAIMG AVEAYRYGGG VGDFGRELDT LYPGGPFDPL GLA NDPDAL AELKVKELKN GRLAMVAMLG FYVQPLVTKA GPVENLTFHL ADPSSNNIFS FTSGFAMFAA TGSKWYGPNR PKWL GPLSG GAVPEYLKGE YAGDYGFDTA GLAADPKLFQ RYRDAELQNG RWAMLGVLGC LAPEVLSNVF GVPYPEPVWF KTGAT ILNG GSIDYLANPK LIHASNLLLT LVLELVFFFA AETWREAGEG PLGKAQDKSY PGGVFDPLGL SKDPAAFAEA KVKEVK NGR LAMLAMLGLF VQAGVTGQSP LENLSAHLAN PGVNFWTSYA PTLAMFAASG RKSAAPK

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Macromolecule #11: LHCI-3

MacromoleculeName: LHCI-3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 46.443383 KDa
SequenceString: VYFFSKKMAS SVPLKQLSIV LLSGAAIACI FISDASTSLS TVSPVVQSRT LQRIDNQLKA SRIQTYPGTT LQLRTASSTT LNEVFGKEG KFQLSLLAPL LSTLGAAVAI FMWNKKTQEE TAMFAATGEK LSDWYGPNRK LFLGPLSDGA PEHLKGELPG D YGFDVLGL ...String:
VYFFSKKMAS SVPLKQLSIV LLSGAAIACI FISDASTSLS TVSPVVQSRT LQRIDNQLKA SRIQTYPGTT LQLRTASSTT LNEVFGKEG KFQLSLLAPL LSTLGAAVAI FMWNKKTQEE TAMFAATGEK LSDWYGPNRK LFLGPLSDGA PEHLKGELPG D YGFDVLGL ATQPTRLERY RQGEIINGRW AMLGIVGCIV PELLARNYGV PFPEPVWFKT GATVFSEEGL NYLGNPSLIH AK SIAAILV TEILFVGAAE AFRVSGGPLG PATDLVYPGK AFDPLGLSKD ETAFAELKVK EVKNGRLAML GMLGLFMQGF ATG KGPLQN LADHLADPTG ANIITFHQRV LSDLGGVAMF AATGEKLSDW YGPNRKLFLG PLSDGAPEHL KGELPGDYGF DVLG LATQP TRLERYRQGE IINGRWAMLG IVGCIV

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Macromolecule #12: LHCI-4

MacromoleculeName: LHCI-4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 44.705488 KDa
SequenceString: IPELLGRGVW FQAGESVDAA QLGLYFMFLA APSEYWRGNG GFGWDQKEKK AGNRIYPGFD PLKMTSDETK TKEIKNGRLA MIAFLGLVS QANTTGVSPF QNLAAVFGAS PVAMFTTTGE KRPLWFPGAK PPAYLTGEFP ADRGFDPLGL AKDPATYERM R SSEVFHSR ...String:
IPELLGRGVW FQAGESVDAA QLGLYFMFLA APSEYWRGNG GFGWDQKEKK AGNRIYPGFD PLKMTSDETK TKEIKNGRLA MIAFLGLVS QANTTGVSPF QNLAAVFGAS PVAMFTTTGE KRPLWFPGAK PPAYLTGEFP ADRGFDPLGL AKDPATYERM R SSEVFHSR LAMLGVVGSL IPELQGQGAW YTLSEKQFGP GPNGEVIGFT ELALIGMLFS YPLEYWRGNG GFGWFEEKGD RT YPGFDPL QLTSEYTKTA EIKNGRLAMS ALLGFAVQHA TTGASPLENW AATTGGSVAM FAAAGERATW FPGAKAPPHL TGE FPGDRG FDPVDFAANP ESFERMRASE VFHGRMAMLG VAGCLIPELL GRGVWFQAGE SVDAAQLGLY FMFLAAPSEY WRGN GGFGW DQKEKK

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Macromolecule #13: Chloroplast light-harvesting complex I protein

MacromoleculeName: Chloroplast light-harvesting complex I protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 27.13065 KDa
SequenceString: WRGNGGFGWF EEKGDRTYPG FDPLQLTSEY TKTAEIKNGR LAMSALLGFA VQHATTGASP LENWAATTGG SVAMFAAAGE RATWFPGAK APPHLTGEFP GDRGFDPVDF AANPESFERM RASEVFHGRM AMLGVAGCLI PELLGRGVWF QAGESVDAAQ L GLYFMFLA ...String:
WRGNGGFGWF EEKGDRTYPG FDPLQLTSEY TKTAEIKNGR LAMSALLGFA VQHATTGASP LENWAATTGG SVAMFAAAGE RATWFPGAK APPHLTGEFP GDRGFDPVDF AANPESFERM RASEVFHGRM AMLGVAGCLI PELLGRGVWF QAGESVDAAQ L GLYFMFLA APSEYWRGNG GFGWDQKEKK AGNRIYPGFD PLKMTSDETK TKEIKNGRLA MIAFLGLVSQ ANTTGVSPFQ NL AAVFGAS PVAML

UniProtKB: Chloroplast light-harvesting complex I protein

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Macromolecule #14: LHCI-6

MacromoleculeName: LHCI-6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 95.660984 KDa
SequenceString: YFFSDKKMYG TVSASSSNKA TSTVAVCACA AVFAVAGFVA VQPRSLYAPA AVRPVVQATM TTVPVAHSVQ SNTVAAQIQS RPLNVESNV FAQVGSTFAP IALGVGALAA FVAALIHKGQ QPVAMAASSG ERLLWIPNAT PPAHLTGEFP GDRGFDPLGL S KDPKVFAR ...String:
YFFSDKKMYG TVSASSSNKA TSTVAVCACA AVFAVAGFVA VQPRSLYAPA AVRPVVQATM TTVPVAHSVQ SNTVAAQIQS RPLNVESNV FAQVGSTFAP IALGVGALAA FVAALIHKGQ QPVAMAASSG ERLLWIPNAT PPAHLTGEFP GDRGFDPLGL S KDPKVFAR MRISEVFHGR LAMLGIVGCV GQEWLFNKGA WFDYSDFDLP RLGLIALQVI APLEYWRGNG GFSWNGNDGP DR SYPGFDP LGLTTEDTKL REIKNGRLAM SAMLGLEVQS HITGKSPLTN LGDHLSSPFT ANILTGGGSV AMFSTSGKVD RPL WFPGGY APSYLTGQYF GDRGFDPAGL AADPKVFERM RVSEVYHGRL AMLAIVGAVV PDILGKGAWY EAAQNAGIGV NEVA VFTAA YGVVEVARGL KANSDPTKNY PGFDPLKLTT DYTKEAEIKN GRLALTGMLG LEVQRHVTGV SPLVNLVEHV KHPLN HNIA ESVMHQWPVA MFAATGHKDG VWFPGAQPPA HLTGEYPADR GFDPLSLAAD PTVYARMRVS EVFHARLSML AIVGSI VPE LLGKGAWFEV GNSVDGIKLG FILMAIAAPT EYWRGNGGFN WDKGTADRSY PGFDPLKLTT DYTKAAEIKN GRLAMTG LL GLTFQYLATG ESPLANLAAH LANPVGANIT TTLAMYSTSG EKYRGLWFPN ITPPAYLTGE FPADRGFDPA GLAADPKV Y ERMRVAEVFN GRLAMLAIVG CVYPELLGNG VWFEVWNKVD FYRFALISLQ VVAPLEYWRG NGGFGWDGEE KYDRSYPGF DPCNLTTEYT KAAEIKNGRL AMIGMFGLEV QNHVTAQGPV ANLIEHLRHP LAANIGASLA HPWPPVAMFA TTGHKDGVWF PGAQPPAHL

+
Macromolecule #15: LHCI-7

MacromoleculeName: LHCI-7 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 66.506625 KDa
SequenceString: EIKNGRLAMT AMLGLEVQSH ITGKSPLTNL SEHLSHPLSA NLLTGGGSLA MFSTAGQKTD RRPLWFPGGY APSWLTGQHF GDRGFDPAG LAADPKVFER MRVSEVYHGR LAMLAIVGAV VPDIQGKGAW YEAAQSAGIG VNEVAVFTAA YGIAEVARGL K ANSDPTSR ...String:
EIKNGRLAMT AMLGLEVQSH ITGKSPLTNL SEHLSHPLSA NLLTGGGSLA MFSTAGQKTD RRPLWFPGGY APSWLTGQHF GDRGFDPAG LAADPKVFER MRVSEVYHGR LAMLAIVGAV VPDIQGKGAW YEAAQSAGIG VNEVAVFTAA YGIAEVARGL K ANSDPTSR YPGFDPLNLT TDYTKEAEIK NGRLALTAML GLEVQRHVTG VSPLVNLVEH VKHPLGHNIA ESVMHQWPVA MF AATGHKD GVWFPGATPP AHLTGEYPAD RGFDPLSLAA DPTVYARMRV SEVFHARLSM LAIVGAIVPE VLGKGAWFEA GNS VDGIKL GFIAMAIAAP TEYWRGNGGF NWDKGAADRS YPGFDPLKLT TDYTKAAEIK NGRLAMAGLL GLTFQYLATG ESPL ANLAA HLANPVGANI TTTLAMYSTS GEKYRGLWFP NITPPAYLTG EFPADRGFDP AGLAADPKVY ERMRIAEVFN GRLAM LAIV GCVYPELLGN GVWFEVWNKV DFYRFALISL QVVAPLEYWR GNGGFGWDGE EKYDRSYPGF DPCNLTTEYT KAAEIK NGR LAMIGMFGLE VQSHVTAQGP VANLIEHLRH PLAANIGANL AHPWPPVAMF ATT

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Macromolecule #16: LHCI-8

MacromoleculeName: LHCI-8 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 89.149461 KDa
SequenceString: FFSIEKKMYG AAHNSSSNKN ATSIVAFFGC AAVFAVAGFV AAQPGALYAP ASVRPAVASM TAAPAMMIQR PSSAVAATNV QAQNVQGSG YHQVGATFAP IVLGVGAITA FVAALLHRGQ KPVAMAATTG ERLLWVPNAT PPAHLTGEFP GDRGFDPLGL A KDPKVYQR ...String:
FFSIEKKMYG AAHNSSSNKN ATSIVAFFGC AAVFAVAGFV AAQPGALYAP ASVRPAVASM TAAPAMMIQR PSSAVAATNV QAQNVQGSG YHQVGATFAP IVLGVGAITA FVAALLHRGQ KPVAMAATTG ERLLWVPNAT PPAHLTGEFP GDRGFDPLGL A KDPKVYQR MRISEVFHGR LAMLGIVGCV APELFFSKGA WFDYSDYDLN RLGLIALQVI APLEYWRGNG GFSWDGNDGP DR SYPGFDP LGLTNEETKL QEIKNGRLAM TAMLGLEVQS HITGKSPLTN LSEHLSHPLS ANLLTGGGSL AMFSTAGQKT DRR PLWFPG GYAPSWLTGQ HFGDRGFDPA GLAADPKVFE RMRVSEVYHG RLAMLAIVGA VVPDIQGKGA WYEAAQSAGI GVNE VAVFT AAYGIAEVAR GLKANSDPTS RYPGFDPLNL TTDYTKEAEI KNGRLALTAM LGLEVQRHVT GVSPLVNLVE HVKHP LGHN IAESVMHQWP VAMFAATGHK DGVWFPGATP PAHLTGEYPA DRGFDPLSLA ADPTVYARMR VSEVFHARLS MLAIVG SIV PELLGKGAWF EVGNSVDGIK LGFILMAIAA PTEYWRGNGG FNWDKGTADR SYPGFDPLKL TTDYTKAAEI KNGRLAM TG LLGLTFQYLA TGESPLANLA AHLANPVGAN ITTTLAMYST SGEKYRGLWF PNITPPAYLT GEFPADRGFD PAGLAADP K VYERMRVAEV FNGRLAMLAI VGCVYPELLG NGVWFEVWNK VDFYRFALIS LQVVAPLEYW RGNGGFGWDG EEKYDRSYP GFDPCNLTTE YTKAAEIKNG RLAMIGMF

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Macromolecule #17: LHCI-9

MacromoleculeName: LHCI-9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 94.434281 KDa
SequenceString: GFVAAQPGAL YAPASVRPAV ASMTAAPAMM IQRPSSAVAA TNVQAQNVQG SGYHQVGATF APIVLGVGAI TAFVAALLHR GQKPVAMAA TTGERLLWIP NATPPAHLTG EFPGDRGFDP LGLAKDPKVY QRMRISEVFH GRLAMLGIVG CVAPELFFSK G AWFDYSDY ...String:
GFVAAQPGAL YAPASVRPAV ASMTAAPAMM IQRPSSAVAA TNVQAQNVQG SGYHQVGATF APIVLGVGAI TAFVAALLHR GQKPVAMAA TTGERLLWIP NATPPAHLTG EFPGDRGFDP LGLAKDPKVY QRMRISEVFH GRLAMLGIVG CVAPELFFSK G AWFDYSDY DLNRLGLIAL QVIAPLEYWR GNGGFSWDGN DGPDRSYPGF DPLGLTNEET KLQEIKNGRL AMTAMLGLEV QS HITGKSP LTNLSEHLSH PLSANLLTGG GSLAMFSTAG QKTDRRPLWF PGGYAPSWLT GQHFGDRGFD PAGLAADPKV FER MRVSEV YHGRLAMLAI VGAVVPDIQG KGAWYEAAQS AGIGVNEVAV FTAAYGIAEV ARGLKANSDP TSRYPGFDPL NLTT DYTKE AEIKNGRLAL TAMLGLEVQR HVTGVSPLVN LVEHVKHPLG HNIAESVMHQ WPVAMFAATG HKDGVWFPGA TPPAH LTGE YPADRGFDPL SLAADPTVYA RMRVSEVFHA RLCMLAIVGA IVPEVLGKGA WFEAGNSVDG IKLGFIAMAI AAPTEY WRG NGGFNWDKGA ADRSYPGFDP LKLTTDYTKA AEIKNGRLAM AGLLGLTFQY LATGESPLAN LAAHLANPVG TNITTTL AM YSTSGEKYRG LWFPNITPPA YLTGEFPADR GFDPAGLAAD PKVYERMRIA EVFNGRLAML AIVGCVYPEL LGNGVWFE V WNKVDFYRFA LISLQVVAPL EYWRGNGGFG WDGEEKYDRS YPGFDPCNLT TEYTKAAEIK NGRLAMIGMF GLEVQSHVT AQGPVANLIE HLRPCSWSVR LESYTPVCWH APGFFQNFQR MGQRAPFQWG VTEPPSFIHT SATVNEGWWG SES

+
Macromolecule #18: LHCI-10

MacromoleculeName: LHCI-10 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 69.436812 KDa
SequenceString: MSAMLGLEVQ SHITGKSPLT NLGDHLSSPF TANILTGGGS VAMFSTSGKV DRPLWFPGGY APSYLTGQYF GDRGFDPAGL AADPKVFER MRVSEVYHGR LAMLAIVGAV VPDILGKGAW YEAAQNAGIG VNEVAVFTAA YGVVEVARGL KANSDPTKNY P GFDPLKLT ...String:
MSAMLGLEVQ SHITGKSPLT NLGDHLSSPF TANILTGGGS VAMFSTSGKV DRPLWFPGGY APSYLTGQYF GDRGFDPAGL AADPKVFER MRVSEVYHGR LAMLAIVGAV VPDILGKGAW YEAAQNAGIG VNEVAVFTAA YGVVEVARGL KANSDPTKNY P GFDPLKLT TDYTKEAEIK NGRLALTGML GLEVQRHVTG VSPLVNLVEH VKHPLNHNIA ESVMHQWPVA MFAATGHKDG VW FPGAQPP AHLTGEYPAD RGFDPLSLAA DPTVYARMRV SEVFHARLSM LAIVGSIVPE LLGKGAWFEV GNSVDGIKLG FIL MAIAAP TEYWRGNGGF NWDKGTADRS YPGFDPLKLT TDYTKAAEIK NGRLAMTGLL GLTFQYLATG ESPLANLAAH LANP VGANI TTTLAMYSTS GEKYRGLWFP NITPPAYLTG EFPADRGFDP AGLAADPKVY ERMRVAEVFN GRLAMLAIVG CVYPE LLGN GVWFEVWNKV DFYRFALISL QVVAPLEYWR GNGGFGWDGE EKYDRSYPGF DPCNLTTEYT KAAEIKNGRL AMIGMF GLE VQNHVTAQGP VANLIEHLRH PLAANIGANL AHPWPPVAMF ATTGHKDGVW FPGAQPPAHL TGEYPADRGF DPLSLAA DP T

+
Macromolecule #19: LHCI-11

MacromoleculeName: LHCI-11 / type: protein_or_peptide / ID: 19 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 112.373086 KDa
SequenceString: FFSDKKMYGT VSASSSNKAT STVAVCACAA VFAVAGFVAV QPRSLYAPAA VRPVVQATMT TVPVAHSVQS NTVAAQIQSR PLNVESNVF AQVGSTFAPI ALGVGALAAF VAALIHKGQQ PVAMAASSGE RLLWIPNATP PAHLTGEFPG DRGFDPLGLS K DPKVFARM ...String:
FFSDKKMYGT VSASSSNKAT STVAVCACAA VFAVAGFVAV QPRSLYAPAA VRPVVQATMT TVPVAHSVQS NTVAAQIQSR PLNVESNVF AQVGSTFAPI ALGVGALAAF VAALIHKGQQ PVAMAASSGE RLLWIPNATP PAHLTGEFPG DRGFDPLGLS K DPKVFARM RISEVFHGRL AMLGIVGCVG QEWLFNKGAW FDYSDFDLPR LGLIALQVIA PLEYWRGNGG FSWNGNDGPD RS YPGFDPL GLTTEDTKLR EIKNGRLAMS AMLGLEVQSH ITGKSPLTNL GDHLSSPFTA NILTGGGSVA MFSTSGKVDR PLW FPGGYA PSYLTGQYFG DRGFDPAGLA ADPKVFERMR VSEVYHGRLA MLAIVGAVVP DILGKGAWYE AAQNAGIGVN EVAV FTAAY GVVEVARGLK ANSDPTKNYP GFDPLKLTTD YTKEAEIKNG RLALTGMLGL EVQRHVTGVS PLVNLVEHVK HPLNH NIAE SVMHQWPVAM FAATGHKDGV WFPGAQPPAH LTGEYPADRG FDPLSLAADP TVYARMRVSE VFHARLSMLA IVGSIV PEL LGKGAWFEVG NSVDGIKLGF ILMAIAAPTE YWRGNGGFNW DKGTADRSYP GFDPLKLTTD YTKAAEIKNG RLAMTGL LG LTFQYLATGE SPLANLAAHL ANPVGANITT TLAMYSTSGE KYRGLWFPNI TPPAYLTGEF PADRGFDPAG LAADPKVY E RMRIAEVFNG RLAMLAIVGC VYPELLGNGV WFEVWNKVDF YRFALISLQV VAPLEYWRGN GGFGWDGEEK YDRSYPGFD PCNLTTEYTK AAEIKNGRLA MIGMFGLEVQ SHVTAQGPVA NLIEHLRHPL AANIGANLAH PWPPVAMFAT TGHKDGVWFP GATPPAHLT GEYPADRGFD PLSLAADPTV YARMRVSEVF HARLSMLAIV GAIVPEVLGK GAWFEAGNSV DGIKLGFIAM A IAAPTEYW RGNGGFNWDK GAADRSYPGF DPLKLTTDYT KAAEIKNGRL AMAGLLGLTF QYLATGESPL ANLAAHLANP VG ANITTTL A

+
Macromolecule #20: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 20 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 236 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #22: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 22 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #23: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 23 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 17 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 25 / Number of copies: 14 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #26: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 26 / Number of copies: 42 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #28: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

MacromoleculeName: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
type: ligand / ID: 28 / Number of copies: 26 / Formula: DD6
Molecular weightTheoretical: 582.855 Da
Chemical component information

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

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Macromolecule #29: water

MacromoleculeName: water / type: ligand / ID: 29 / Number of copies: 44 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
20.0 mMMES
0.03 %Sucrose monolaurate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / 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: 1.2 µm / Nominal magnification: 60000

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Image processing

Particle selectionNumber selected: 507565
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: An initial model was generated de novo from the 2D classified good particles.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 56060
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: ModelAngelo
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9vfj:
PSI-LHCI of Euglena gracilis strain Z

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