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- EMDB-65121: Cryo-EM structure of Euglenophyte photosystem I -

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Basic information

Entry
Database: EMDB / ID: EMD-65121
TitleCryo-EM structure of Euglenophyte photosystem I
Map dataCryo-EM structure of euglenophyte photosystem I
Sample
  • Complex: Cryo-EM structure of Euglenophyte photosystem I
    • Protein or peptide: x 18 types
  • Ligand: x 11 types
KeywordsEuglenophyte / Photosystem I / evolution / 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) / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaA / 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 / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center / Light harvesting chlorophyll a /b binding protein of PSII
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsZhao LS / Qin BY / Li K / Liu LN / Zhang YZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Euglenophyte photosystem I
Authors: Zhao LS / Qin BY / Li K / Zhang YZ / Liu LN
History
DepositionJun 21, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65121.png

Downloads & links

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Map

FileDownload / File: emd_65121.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of euglenophyte photosystem I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 417.2 Å		0.83 Å/pix.
x 500 pix.
= 417.2 Å		0.83 Å/pix.
x 500 pix.
= 417.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8344 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.46309224 - 1.4432801
Average (Standard dev.)0.0162277 (±0.03804578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 417.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of euglenophyte photosystem I

Fileemd_65121_half_map_1.map
AnnotationCryo-EM structure of euglenophyte photosystem I
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of euglenophyte photosystem I

Fileemd_65121_half_map_2.map
AnnotationCryo-EM structure of euglenophyte photosystem I
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Euglenophyte photosystem I

EntireName: Cryo-EM structure of Euglenophyte photosystem I
Components
  • Complex: Cryo-EM structure of Euglenophyte photosystem I
    • 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: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: LHC-1
    • Protein or peptide: Light harvesting chlorophyll a /b binding protein of PSII
    • Protein or peptide: LHC-3
    • Protein or peptide: Chloroplast light-harvesting complex I protein
    • Protein or peptide: Chloroplast light-harvesting complex I protein
    • Protein or peptide: Chloroplast light-harvesting complex I protein
    • Protein or peptide: Chloroplast light-harvesting complex I protein
    • Protein or peptide: LHC-10, 15
    • Protein or peptide: LHC-11
    • Protein or peptide: Chloroplast light-harvesting complex I protein
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: BETA-CAROTENE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CHLOROPHYLL B
  • 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

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Supramolecule #1: Cryo-EM structure of Euglenophyte photosystem I

SupramoleculeName: Cryo-EM structure of Euglenophyte photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 760 KDa

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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 / EC number: photosystem I
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 84.059406 KDa
SequenceString: MTITPPEQQV KRVRVAFVSN PVETSFEKWS RPGHFSRLLS KGPNTTTWIW NLHADAHDFD NHTTDLEDIS RKVFSAHFGQ LAIIEIWLS GMFFHGARFS NYEAWLLDPI HVKPSAQIVW PIVGQEILNG DVGGNFQGIQ ITSGLFQLWR SCGITSEFQL Y ITALTGLI ...String:
MTITPPEQQV KRVRVAFVSN PVETSFEKWS RPGHFSRLLS KGPNTTTWIW NLHADAHDFD NHTTDLEDIS RKVFSAHFGQ LAIIEIWLS GMFFHGARFS NYEAWLLDPI HVKPSAQIVW PIVGQEILNG DVGGNFQGIQ ITSGLFQLWR SCGITSEFQL Y ITALTGLI FSAVLFFAGW FHYHKAAPKL EWFQNVESML NHHLSGLLGL GCLSWAGHQI HVSLPINKLL DSGVNPAELP LP HDFILDK SLISQLYPSF SKGLAPFFTF HWSEYSDFLT FRGGLNNVTG GLWLTDVAHH HLALAVLFIL AGHMYKTNWK IGH DIKGLL ESHTGPFTGQ GHKGLYEIFT NSWHAQLSLN LAMMGSLSII VAQHMYSMPP YPYIAIDYGT ELSLFTHHYW IGGF CIVGA AAHAAIFMVR DYDPALNFNN LLDRVLLHRD AIISHLNWVC IFLGLHSFGL YIHNDTLSAL GRPQDMFSDS AIQLQ PVFA QWIQNTHYLA PTLTAFNLVS PTTPVWGGDV VSISGKVAMM PIKLGTADFL VHHIHAFTIH VTVLILLKGV LFSRSS RLI PDKASLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSI SVAIFHFSWK MQSDVWGTVL ANKVSHITGG NFSQGSL TI NGWLRDFLWA QSSQVIQSYG SPLSAYGLMF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPN IQPRALSI T QGRAVGVAHY LLGGIATTWS FFLARIISVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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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: 82.723211 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 KF

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: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 22.389361 KDa
SequenceString: MFAETGEKAA KPAWTVPDLA DALKNTSAVA KAKGIATQLP TFWELRDALS EVPKSKFPEV FASYKGSTGT LLSAAEKEEK YVITWTSPK KQIFELPTGG AAEMEEGENI FYFARKEQCL ALGAQLRTAF KPRIENFQIF RVFPNGEVQY LHPKDGVFPE K VNQGRTKA ...String:
MFAETGEKAA KPAWTVPDLA DALKNTSAVA KAKGIATQLP TFWELRDALS EVPKSKFPEV FASYKGSTGT LLSAAEKEEK YVITWTSPK KQIFELPTGG AAEMEEGENI FYFARKEQCL ALGAQLRTAF KPRIENFQIF RVFPNGEVQY LHPKDGVFPE K VNQGRTKA NHNPRSIGEN AEPASVKFTG TTPKDVQTEG AVAMF

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Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 11.251521 KDa
SequenceString:
MITRLADDAA ARVADRTQFI EEYKERRAEA PATPKAKAGP ARGSTVKVTR PESYWYNQYG KVISVDESGA IRYPVVVRFE KENYQGVTT NNFALDELEY

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Macromolecule #6: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 18.556314 KDa
SequenceString:
MPANATEAIL GLTPCAESAK FQKVLTKEVK ALEKREKLYE PGSAPFQALE ATKAKTQARF AKYAESGLLC GADGLPHLIS DPGLAVKYG HAGETLIPTI GFLYVAGYIG TAGRTYLQEI STRQKPTQSE IIIDVPLATS IAFKSWDWPN KAVKELASGT L LEDAKNVP VSRR

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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: LHC-1

MacromoleculeName: LHC-1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 22.417451 KDa
SequenceString: MLATSGEKRP TWFPGAEAPA WLTGEFPGDR GFDPCGLARD PVDFAKFRDS EVFHGRWAML GLVGCLVPEV FGNLGIAQLP AWYDAATVA NTSNLDYLGN PNLIHASNVS FIALSTLLLM GPVEAWRWNG ALASEAKSAE RTTYPGGPFD PLKLGASPEL K LKEIKNGR ...String:
MLATSGEKRP TWFPGAEAPA WLTGEFPGDR GFDPCGLARD PVDFAKFRDS EVFHGRWAML GLVGCLVPEV FGNLGIAQLP AWYDAATVA NTSNLDYLGN PNLIHASNVS FIALSTLLLM GPVEAWRWNG ALASEAKSAE RTTYPGGPFD PLKLGASPEL K LKEIKNGR LAMVGMFGFW AQSYVTGEGP LANLAAHLAD PAHNNLLNTV A

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Macromolecule #10: Light harvesting chlorophyll a /b binding protein of PSII

MacromoleculeName: Light harvesting chlorophyll a /b binding protein of PSII
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 24.103516 KDa
SequenceString: MFAATGSKWY GPNRPKWLGP LSGGAVPEYL KGEYAGDYGF DTAGLAADPK LFQRYRDAEL QNGRWAMLGV LGCLAPEVLS NVFGVPYPE PVWFKTGATI LNGGSIDYLA NPKLIHASNL LLTLVLELVF FFAAETWREA GEGPLGKAQD KSYPGGVFDP L GLSKDPAA ...String:
MFAATGSKWY GPNRPKWLGP LSGGAVPEYL KGEYAGDYGF DTAGLAADPK LFQRYRDAEL QNGRWAMLGV LGCLAPEVLS NVFGVPYPE PVWFKTGATI LNGGSIDYLA NPKLIHASNL LLTLVLELVF FFAAETWREA GEGPLGKAQD KSYPGGVFDP L GLSKDPAA FAEAKVKEVK NGRLAMLAML GLFVQAGVTG QSPLENLSAH LANPGVNFWT SYAPTLA

UniProtKB: Light harvesting chlorophyll a /b binding protein of PSII

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Macromolecule #11: LHC-3

MacromoleculeName: LHC-3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 24.694389 KDa
SequenceString: MFAATGEKLS DWYGPNRKLF LGPLSDGAPE HLKGELPGDY GFDVLGLATQ PTRLERYRQG EIINGRWAML GIVGCIVPEL LARNYGVPF PEPVWFKTGA TVFSEEGLNY LGNPSLIHAK SIAAILVTEI LFVGAAEAFR VSGGPLGPAT DLVYPGKAFD P LGLSKDET ...String:
MFAATGEKLS DWYGPNRKLF LGPLSDGAPE HLKGELPGDY GFDVLGLATQ PTRLERYRQG EIINGRWAML GIVGCIVPEL LARNYGVPF PEPVWFKTGA TVFSEEGLNY LGNPSLIHAK SIAAILVTEI LFVGAAEAFR VSGGPLGPAT DLVYPGKAFD P LGLSKDET AFAELKVKEV KNGRLAMLGM LGLFMQGFAT GKGPLQNLAD HLADPTGANI ITFHQRVLSD LG

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Macromolecule #12: Chloroplast light-harvesting complex I protein

MacromoleculeName: Chloroplast light-harvesting complex I protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 19.968424 KDa
SequenceString:
MFTTTGEKRP VWFPGATPPA YLTGEFPADR GFDPLGLAKD PATYERMRSS EVFHSRLAML GVVGSLIPEL QGQGAWYTLS EKQFGPGPN GEVIGFTELA LIGMLFSYPL EYWRGNGGFG WFEEKGDRTY PGFDPLQLTS EYTKTAEIKN GRLAMSALLG F AVQHATTG ASPLENWAAT TGGSVA

UniProtKB: Chloroplast light-harvesting complex I protein

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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: 19.103709 KDa
Recombinant expressionOrganism: Euglena gracilis (euglena)
SequenceString:
MFAAAGERAT WFPGAKAPPH LTGEFPGDRG FDPVDFAANP ESFERMRASE VFHGRMAMLG VAGCLIPELL GRGVWFQAGE SVDAAQLGL YFMFLAAPSE YWRGNGGFGW DQKEKKAGNR IYPGFDPLKM TSDETKTKEI KNGRLAMIAF LGLVSQANTT G VSPFQNLA AVFGASPVA

UniProtKB: Chloroplast light-harvesting complex I protein

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Macromolecule #14: Chloroplast light-harvesting complex I protein

MacromoleculeName: Chloroplast light-harvesting complex I protein / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.021699 KDa
SequenceString:
MAASSGERLL WIPNATPPAH LTGEFPGDRG FDPLGLSKDP KVFARMRISE VFHGRLAMLG IVGCVGQEWL FNKGAWFDYS DFDLPRLGL IALQVIAPLE YWRGNGGFSW NGNDGPDRSY PGFDPLGLTT EDTKLREIKN GRLAMSAMLG LEVQSHITGK S PLTNLGDH LSSPFTANIL TGGGSVA

UniProtKB: Chloroplast light-harvesting complex I protein

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Macromolecule #15: Chloroplast light-harvesting complex I protein

MacromoleculeName: Chloroplast light-harvesting complex I protein / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 21.290225 KDa
SequenceString:
MYSTSGEKYR GLWFPNITPP AYLTGEFPAD RGFDPAGLAA DPKVYERMRI AEVFNGRLAM LAIVGCVYPE LLGNGVWFEV WNKVDFYRF ALISLQVVAP LEYWRGNGGF GWDGEEKYDR SYPGFDPCNL TTEYTKAAEI KNGRLAMIGM FGLEVQSHVT A QGPVANLI EHLRHPLAAN IGANLAHPWP PVA

UniProtKB: Chloroplast light-harvesting complex I protein

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Macromolecule #16: LHC-10, 15

MacromoleculeName: LHC-10, 15 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.346094 KDa
SequenceString:
MFSTAGQKTD RRPLWFPGGY APSWLTGQHF GDRGFDPAGL AADPKVFERM RVSEVYHGRL AMLAIVGAVV PDIQGKGAWY EAAQSAGIG VNEVAVFTAA YGIAEVARGL KANSDPTSRY PGFDPLNLTT DYTKEAEIKN GRLALTAMLG LEVQRHVTGV S PLVNLVEH VKHPLGHNIA ESVMHQWPVA

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Macromolecule #17: LHC-11

MacromoleculeName: LHC-11 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 20.130818 KDa
SequenceString:
MAATTGERLL WIPNATPPAH LTGEFPGDRG FDPLGLAKDP KVYQRMRISE VFHGRLAMLG IVGCVAPELF FSKGAWFDYS DYDLNRLGL IALQVIAPLE YWRGNGGFSW DGNDGPDRSY PGFDPLGLTN EETKLQEIKN GRLAMTAMLG LEVQSHITGK S PLTNLSEH LSHPLSANLL TGGGSLA

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Macromolecule #18: Chloroplast light-harvesting complex I protein

MacromoleculeName: Chloroplast light-harvesting complex I protein / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 18.443971 KDa
SequenceString:
MFATTGHKDG VWFPGATPPA HLTGEYPADR GFDPLSLAAD PTVYARMRVS EVFHARLSML AIVGAIVPEV LGKGAWFEAG NSVDGIKLG FIAMAIAAPT EYWRGNGGFN WDKGAADRSY PGFDPLKLTT DYTKAAEIKN GRLAMAGLLG LTFQYLATGE S PLANLAAH LANPVG

UniProtKB: Chloroplast light-harvesting complex I protein

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 244 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #21: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 21 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #22: (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: 22 / Number of copies: 37 / 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 #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 13 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #24: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 3 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 16 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #26: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 26 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 28 / Number of copies: 27 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #29: (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: 29 / Number of copies: 1 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 78124
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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