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- EMDB-62242: PSI-LHCI of the red alga Galdieria sulphuraria NIES-3638 -

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Basic information

Entry
Database: EMDB / ID: EMD-62242
TitlePSI-LHCI of the red alga Galdieria sulphuraria NIES-3638
Map data
Sample
  • Complex: PSI-LHCI
    • Protein or peptide: x 20 types
  • Ligand: x 12 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding ...plastid thylakoid membrane / thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...Photosystem I PsaO / PsaO transmembrane domain / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / Electron transport accessory-like domain superfamily / 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
Photosystem I subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / PSI-K / Photosystem I reaction center subunit XI ...Photosystem I subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / PSI-K / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Light-harvesting complex protein / Uncharacterized protein / Photosystem I subunit O / Uncharacterized protein / Light-harvesting complex protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsKato K / Nakajima Y / Shen JR / Nagao R
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K14211 Japan
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
Japan Society for the Promotion of Science (JSPS)JP23H02423 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Structure of a photosystem I supercomplex from close to an ancestral red alga.
Authors: Koji Kato / Minoru Kumazawa / Yoshiki Nakajima / Takehiro Suzuki / Naoshi Dohmae / Jian-Ren Shen / Kentaro Ifuku / Ryo Nagao /
Abstract: Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, ...Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of NIES-3638 at 2.19-angstrom resolution using cryo-electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll /-binding-like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.
History
DepositionNov 1, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62242.png

Downloads & links

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Map

FileDownload / File: emd_62242.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 320 pix.
= 240.64 Å		0.75 Å/pix.
x 320 pix.
= 240.64 Å		0.75 Å/pix.
x 320 pix.
= 240.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.056990836 - 0.16694579
Average (Standard dev.)0.00032227056 (±0.0041305195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 240.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62242_additional_1.map
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Half map: #2

Fileemd_62242_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62242_half_map_2.map
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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 subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PSI-K
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I subunit O
    • Protein or peptide: Psa28
    • Protein or peptide: RedCAP
    • Protein or peptide: Light-harvesting complex protein
    • Protein or peptide: Light-harvesting complex protein
    • Protein or peptide: Light-harvesting complex protein
    • Protein or peptide: Light-harvesting complex protein
    • Protein or peptide: Light-harvesting complex protein
    • Protein or peptide: Light-harvesting complex protein
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: Coenzyme Q4
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: UNKNOWN LIGAND
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: Zeaxanthin
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: water

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Supramolecule #1: PSI-LHCI

SupramoleculeName: PSI-LHCI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 680 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: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 82.528977 KDa
SequenceString: KVLIDRNVVP TNFEKWSKPG HFSRSLAKGP KTTTWIWNLH ADAHDFDSHT NSLEEISRKI FSAHFGQLAV IFIWLSGMYF HGAKFSNYV AWLNNPINIK PSAQVVWPII GQEILNADVG GGFQGIQITS GLFQLWRASG ITNEMQLYVT AIGGLFMASL M LFAGWFHY ...String:
KVLIDRNVVP TNFEKWSKPG HFSRSLAKGP KTTTWIWNLH ADAHDFDSHT NSLEEISRKI FSAHFGQLAV IFIWLSGMYF HGAKFSNYV AWLNNPINIK PSAQVVWPII GQEILNADVG GGFQGIQITS GLFQLWRASG ITNEMQLYVT AIGGLFMASL M LFAGWFHY HKAAPKLEWF QNVESMLNHH LAGLLGLGSL GWTGHLIHVS LPINKLLDSG IVPAQIPLPH EFILNRNLMS EL YPSFNKG LLPFFTLNWN EYNDFLTFKG GLNPVTGGLW LTDIAHHHLA IAVIFIIAGH MYRTNWSIGH SLKEILDAHK GPF TGEGHR GLFEILTTSW HAQLAINLAM LGSLSIIVAH HMYAMPPYPY LATDYPTQLS LFTHHMWIGG FCIVGAGAHA AIFM VRDYS PAQNYNNLLD RVIRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMRALGRP QDMFSDVAIQ LQPIFAQWIQ NCHSI APGN TAPNVLATTS YVFGGDIISV GNKIAIMPMS LGTADFMVHH IHAFTIHVTA LILLKGVLFA RNSRLIPDKA NLGFRF PCD GPGRGGTCQV SGWDHVFLGL FWMYNSLSIV IFHFSWKMQS DVWGTISSSG DISHITRGNF AQSAITINGW LRDFLWA QA SQVIQSYGSS SSAYGLMFLG AHFVWAFSLM FLFSGRGYWQ ELIESIVWAH NKLKVAPSIQ PRALSITQGR AVGVAHYL L GGIATTWAFF LARIIAIG

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: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 82.418102 KDa
SequenceString: VTKFPKFSQA LAQDPTTRRI WYGIATAHDF ESHDNITEEN LYQRIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEKWILNP TKIKPIAHA IWDPHFGQAA LKAFSQTGVD YPTNISYSGL YHWWYTIGIR TNNDLYLGAL FLLVISGLFL FAGWLHLQPK F KPSLAWFK ...String:
VTKFPKFSQA LAQDPTTRRI WYGIATAHDF ESHDNITEEN LYQRIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEKWILNP TKIKPIAHA IWDPHFGQAA LKAFSQTGVD YPTNISYSGL YHWWYTIGIR TNNDLYLGAL FLLVISGLFL FAGWLHLQPK F KPSLAWFK NNESRLNHHL AGLFGVSSLA WAGHLVHVAI PEARGQHVGW DNFLSTKPHP AGLEPFFKGQ WSVYADGPDS MN HVFNTSE GAGKAILTFL GGFHPQTKSL WLTDIAHHHL AIAVIFIIAG HMYRTNWSIG HSLKEILDAH RAPGGRLGDG HKG LFETIN NSLHFQLGLA LASLGVITSL VAQHMYAMPS YVFIANDFTT QAALYTHHQY IAGFLMVGAF AHGAIFFIRD YNPE QNKNN VLARMLEHKE AIISHLSWVS LFLGFHTLGI YVHNDVVVAF GSPEKQILIE PVFAQWIQAA SGKALYGFNI LLSSS DSVA TRAGESLWLP GWLKGVNDTN NSLFLDIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAMFWML NTLGWLTFYW HWKHLTLWGG NVNQFNESST YLMGWFRDYL WLNSSPLING YNPYGVN NL SVWAWMFLFG HLVWATGFMF LISWRGYWQE LIETLAWAHE RTPLANLIKW KDKPVALSIV QARLVGLAHF AVGYILTY A PFVIASTVGK F

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: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 8.719128 KDa
SequenceString:
AHNVKIYDTC IGCTQCVRAC PCDVLEMVPW DGCKALQIAS APRTEDCVGC KRCETACPTD FLSIRVYLGA ETSRSMGLAY

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: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 15.669881 KDa
SequenceString:
TLNLKMPSPS FGGSTGGWLR SAENEEKYAI TWISKNEEVF EMPTAGAALM RSGENLLYFA RKEQCLSLGT QLKTQFKIDN YKIYRVFPN GEIQYLHPKD GVFPEKVNEG RKAINTLTRS IGKNPDPVVV KFINKQTFE

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I subunit IV

MacromoleculeName: Photosystem I subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 7.330392 KDa
SequenceString:
MVQKGSKVKI LRKESYWYQE IGNVVTVEKS GIKYPIIVRF DKVNYAGVNT NNFASEEVIE IEAP

UniProtKB: Photosystem I subunit IV

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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: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 18.254176 KDa
SequenceString:
EFNNLIPCKE SKIFNKRLES TIKKLENKLS KYEVGSSSYL AIKNTINKTN NRFHKYMESG VLCGKDGLPH LIADGRWSHA GEFVIPSLL FIYISGWIGW VGRGYLSAIK NTNKAIENEI IIDVPLALKF MSSGFIWPLS ALREYTKGDL LMKDSEVTIS P R

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 3.879621 KDa
SequenceString:
MTASYLPSIL VPIIGLVFPF ISMALFFIYV EQEE

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 4.754694 KDa
SequenceString:
MNKDLLKYLS TAPVLGVIWI AITAAIIVEF NRLYPDALFF PL

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: PSI-K

MacromoleculeName: PSI-K / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 6.874181 KDa
SequenceString:
SASTSIIFIV VNTICIILGK YSIQNKKNQV SLIANINLAE LLASMSLGHI ISSATVIGLK SLNII

UniProtKB: PSI-K

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 15.206506 KDa
SequenceString:
DFIKPYNDDP FVGNLATPIN TSSLTKNLLG NLPIYRRRLS PLLRGLEIGM AHGYFFIGPF YKLGPLRNSE IALLSGFLSC VGLIIFLTV GLLLYGNTSF DKDESKDQLQ TSEGWNQFTA GFLVGAIGGA GFAYLILVNL

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 3.067771 KDa
SequenceString:
MINDSQIFIA LILSLVPAVL ALKLAREL

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 10.52216 KDa
SequenceString:
FQISEDTPFD ANPLVIIVAL LGWTLPASIP SNIPILHGTG LTQAFFTSIQ SNLAEWPKGP ALDDPFWLYM VLWHVGLFIV LFFGTIGYG ISKNRV

UniProtKB: Photosystem I subunit O

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Macromolecule #13: Psa28

MacromoleculeName: Psa28 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 9.030552 KDa
SequenceString:
KDTFWTGKVP PSTVLGIGEK VPSAAYIISS VVCLLVGSYC VYESNLLSPL TVTTINPLYV LGSLLVPYSW GLHVAGWIQL KNGK

UniProtKB: Uncharacterized protein

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Macromolecule #14: RedCAP

MacromoleculeName: RedCAP / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 19.43558 KDa
SequenceString:
LGIFRQAMKD FASEYPDFVS RGLGVTSKAE RWNGRHAMFG LLAIVLTGYA KGHGWIPNAD QVLDMQQWGT LVMEGFNQKI TNERAIVLV AHIHVLLVSI AAAIAPFSFQ DRLLLRPGEK DEEPAGLLPP FKLGLTKEAE LWNGRLAMLG VTFIVATSII T GQSILDVV NKGLGNILY

UniProtKB: Uncharacterized protein

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Macromolecule #15: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 18.228047 KDa
SequenceString:
SRALPFLEAP KKLDGKIPGD AGFDPLYISD NMNLDYLRAS EIKHCRVAML AALGYITQEF FHLPGDVFNE KHALAAIHKV PIEGWIQII LFISLVEIAT FRTTFSFDRE PGDFGFDPLG LAKSPQLRRR YQESEIRNGR LAMIAVIGFI VQELVTGKSV V EQ

UniProtKB: Light-harvesting complex protein

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Macromolecule #16: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 14.670181 KDa
SequenceString:
GFDPLGFSTI IDLRYLRESE LKHCRIAMLA VVGFIVQEFI HLPGDLFSNP HPMQAIGQVP ISGWIQIFLL VAILEMIDIA AIKETLQGN REPGYFGFDP LGLAKDKQAH DRYLLSELKN GRLAMIASIA FM

UniProtKB: Light-harvesting complex protein

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Macromolecule #17: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 19.949285 KDa
SequenceString:
RMSKAIPFFP KPARLDESMP GYAGFDPLGF SDKFDVKFLQ EAEIKHCRIC MLAALGWVVP EFWHLPSEVF SNTSPLAALG QVPKLGLIQ ILLLVLALEA ISLDKITFHP EKEPGDFGFD PLGLGKGNAK KWMQTAELKN GRLAMIAMGA FFHQNLLTNQ G IFEQLRTH NFFPTTFPLH

UniProtKB: Light-harvesting complex protein

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Macromolecule #18: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 19.901129 KDa
SequenceString:
TKSLSVPFLE RPKNLDGTAP GDVGFDPLYI SDLLDIQWLR ESEIKHGRIC MLAAVGFIVQ EFVHLPGEVF SNKVAIDALF QVPSGGLWQ IFLFIGLLEF VMNKGKMTPL DMFSDPNRKP GDFGFDPLGL GKDPQARKRY EVAEIKNGRL AMLAVGGFIH H MLLTHQGV VEQLTHFRSL

UniProtKB: Light-harvesting complex protein

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Macromolecule #19: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 20.512943 KDa
SequenceString:
KPKWSKALPF MLWPQNLDGT MAGDVGFDPF GFTNVFDVKW MREAELKHCR IAMLAALGFI VQELWTFPYP YFSKVPPVLA HDVYVKTGG MSQILLFVIF FEVISLFAVS QMMEGKREPG VFHFDPLGLA KDPDTFRKYE WSELRNGRLA MIAVGGFIHQ Y WVTKQGIF EQLANFRPLS

UniProtKB: Light-harvesting complex protein

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Macromolecule #20: Light-harvesting complex protein

MacromoleculeName: Light-harvesting complex protein / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Galdieria sulphuraria (eukaryote)
Molecular weightTheoretical: 18.787791 KDa
SequenceString:
KSKAIPFLDR PPALDGSMVG DVGFDPLNIS SYLDLRWLRE SEIKHCRIAM LAVVGWFVQE VYHLPNEIYS SSVPTEAFWK TLVTGPMGQ IVLWTSLFEM ISTPAVIQML QGSGREPGYF GFDPLGLGKN PELYKRFQLS ELKNGRLAMI AIGGLIHQSF L THMGAIQQ

UniProtKB: Light-harvesting complex protein

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Macromolecule #21: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 21 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 167 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #23: Coenzyme Q4

MacromoleculeName: Coenzyme Q4 / type: ligand / ID: 23 / Number of copies: 2 / Formula: A1L64
Molecular weightTheoretical: 454.641 Da

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 10 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 24 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 27 / Number of copies: 52 / Formula: UNL
Molecular weightTheoretical: 949.299 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / 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 #29: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 29 / Number of copies: 30 / Formula: 5X6
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

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Macromolecule #30: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 30 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #31: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 31 / Number of copies: 4 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol

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Macromolecule #32: water

MacromoleculeName: water / type: ligand / ID: 32 / Number of copies: 608 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES
0.03 %DDMDDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
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: 2583694
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 2D classification.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 110313
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Phyre2 server
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9kc5:
PSI-LHCI of the red alga Galdieria sulphuraria NIES-3638

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