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- EMDB-36678: PSI-AcpPCI supercomplex from Amphidinium carterae -

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Basic information

Entry
Database: EMDB / ID: EMD-36678
TitlePSI-AcpPCI supercomplex from Amphidinium carterae
Map data
Sample
  • Complex: PSI-AcpPCI supercomplex from Amphidinium carterae
    • Protein or peptide: x 28 types
  • Ligand: x 12 types
KeywordsPhotosysrem I / Photosynthesis / Dinoflagellate
Biological speciesAmphidinium carterae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi ZH / Li XY / Wang WD
Funding support China, 8 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.
Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / ...Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the ...Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) /-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls and and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.
History
DepositionJun 28, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36678.png

Downloads & links

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Map

FileDownload / File: emd_36678.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.5627794 - 1.8833188
Average (Standard dev.)-0.00012137204 (±0.020952491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 665.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36678_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36678_half_map_2.map
Projections & Slices
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Sample components

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Entire : PSI-AcpPCI supercomplex from Amphidinium carterae

EntireName: PSI-AcpPCI supercomplex from Amphidinium carterae
Components
  • Complex: PSI-AcpPCI supercomplex from Amphidinium carterae
    • Protein or peptide: Photosystem I PsaA
    • Protein or peptide: Photosystem I PsaB
    • Protein or peptide: Photosystem I PsaC
    • Protein or peptide: Photosystem I PsaD
    • Protein or peptide: Photosystem I PsaE
    • Protein or peptide: Photosystem I PsaF
    • Protein or peptide: Photosystem I PsaR
    • Protein or peptide: Photosystem I PsaI
    • Protein or peptide: Photosystem I PsaJ
    • Protein or peptide: Photosystem I PsaL
    • Protein or peptide: Photosystem I PsaM
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14
    • Protein or peptide: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • 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: PERIDININ
  • Ligand: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
  • Ligand: Chlorophyll c1Chlorophyll c
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Supramolecule #1: PSI-AcpPCI supercomplex from Amphidinium carterae

SupramoleculeName: PSI-AcpPCI supercomplex from Amphidinium carterae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24, #26, #25, #27-#28
Source (natural)Organism: Amphidinium carterae (eukaryote)

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Macromolecule #1: Photosystem I PsaA

MacromoleculeName: Photosystem I PsaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 70.529703 KDa
SequenceString: DFSKAAFGSA TGLVAKAASQ TTTAIWNLHA DAHDFSNSSY LSKQVFAANL AHIGVVFIWL SGMHFHGAYF SNYLDWLQDP SIAPTAQQV SNIANQSVLN PIRVTSGFFN LWLAEGITST YQLKVIAAFG LIASALCFLG SYFHMHSSTS FTRVLNTKLT S LSTHHLVG ...String:
DFSKAAFGSA TGLVAKAASQ TTTAIWNLHA DAHDFSNSSY LSKQVFAANL AHIGVVFIWL SGMHFHGAYF SNYLDWLQDP SIAPTAQQV SNIANQSVLN PIRVTSGFFN LWLAEGITST YQLKVIAAFG LIASALCFLG SYFHMHSSTS FTRVLNTKLT S LSTHHLVG LLGLGSLAWA GHLIHISLPV NILLNAGVAV PSPHSLLSSK AVATIVEQLS FSALTSSDGY VWQPLVYSAM HH FALALVL IVGSIFLSTA SNPLMSFTVG SSWHLVLGVQ LFVTGTASVL YAQMSNAYPV YPYLLTDHPT VVSLFVHHMW IGG FFLVGA FAHLSIGLVR DTLPQSFSVV LTQRDIILGH LTWVVAFLGV HSFGLYVHND TMQALGRPDD MFSDNAISLL PVFA RWSTL TLNSTGSAVS VLGVELSTAD FMVTHIHAFT IHTTVLILVK GFLYARSSRL VNDKYKLDFR YPCDGPGRGG TCQIS PWDH VFLGLFWMYN SISVVIFHFF WEYQSNLASI KASAGGSIRA LASDFELNSI NTNGWLRNFL WSGAAQVIQS YGSPLA AYG LTFLASHFVW ALSLMFLFSG RGYWQELIES VLWAHHKLYV VPHIQPRALS ITSGRAVGLT HYLLGGIGTT WSFFLAR IV ATA

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Macromolecule #2: Photosystem I PsaB

MacromoleculeName: Photosystem I PsaB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 67.96257 KDa
SequenceString: YGRCATQRYF QVLGNIHDIE LNESLNSPQA IQALSFGQLS VILLWLAAYT FHIGWSGNFE AFIDNPLGVQ PINHFVLDPH YSQYKVDTT IAALTNHPIY HWLMTVGFTS NAQIYRFTLG LEITAAVMLV LSLAPSVGLL SMGGLEVVSW ISICWAGHLV N FAPGAANL ...String:
YGRCATQRYF QVLGNIHDIE LNESLNSPQA IQALSFGQLS VILLWLAAYT FHIGWSGNFE AFIDNPLGVQ PINHFVLDPH YSQYKVDTT IAALTNHPIY HWLMTVGFTS NAQIYRFTLG LEITAAVMLV LSLAPSVGLL SMGGLEVVSW ISICWAGHLV N FAPGAANL TNVVMEGPGS LGNLMNVLTF NGGIQLGTQA LAVSDVAHHH VAIGIVGLWI SALLRVSKYA WNFNTQSSYH LD LSLSLTV GGILTSLLAQ QAYVYPALSY LPYDYLTTTS LYVHHQYIGA FLATGGFVHG GIFLVRDYTL SNDLVGKLLA TKA TVISTL SWITLFLGFH ATGLYMHNDA MAAFGVPQKQ IIIEPVFAEF IQQVFFLGTP VYGLGSAAVS STPTLSFLPI ISGG DFLVH HAIALGLHTT VLVLIKGALD SQGSYLFPDK QSFGYGFACD GPGRGGTCDI STWDSFYLAF FWVNNTVAWF TYYFH WKVL SLWQSSTAVF DENSLYLMGW FRDYLWQNCA ALLSGYDSLG SNDLAVWAWA FLLAHLAWAT GFMFLISWRG YWQELI DTV IYMHLKAPFF NEIWSADVVT PVALSIVQAR FIGLAHYVAG FILTYLAFVV GATS

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Macromolecule #3: Photosystem I PsaC

MacromoleculeName: Photosystem I PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 9.409729 KDa
SequenceString:
AHAVKIYDTC IGCTLCVRAC PTDVIEMVPA TVNAAKQVAS TPRVEDCVGC KRCETACPTD FLSIRVYLQE NEETQYSLGL DLADWS

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Macromolecule #4: Photosystem I PsaD

MacromoleculeName: Photosystem I PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 28.754719 KDa
SequenceString: AVPNTPKSSP DTLAGNRTEA SAVSRPYDKF NVNYPLSSPD QARTEVTTKE IPRPEDLVDS PKFPLFGGSA NGYMSKATRE RHAITWTAK EETTFEMPTS GWAMMNKGEN LCYFRKKEQC IALCKQLRSM KINDVKIYRL SKDGTVTFLH PSDGVFPEKV N KGRVPVNF ...String:
AVPNTPKSSP DTLAGNRTEA SAVSRPYDKF NVNYPLSSPD QARTEVTTKE IPRPEDLVDS PKFPLFGGSA NGYMSKATRE RHAITWTAK EETTFEMPTS GWAMMNKGEN LCYFRKKEQC IALCKQLRSM KINDVKIYRL SKDGTVTFLH PSDGVFPEKV N KGRVPVNF RPFTVCQNAK QGELKFTEYW TKPYEADALT TLFVKARVAA YNDVVNLFPL PNPKLTSGPA EPTSVDYDAL TK EAMEGQK KRIEAAMASV

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Macromolecule #5: Photosystem I PsaE

MacromoleculeName: Photosystem I PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 8.617627 KDa
SequenceString:
AWVGPKKGSQ VRILRPESYW FQQRGTVVNV NQKTNIKYPV TVKFDFVNYA NVNTNGFALW EVDELKEGEY DPDL

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Macromolecule #6: Photosystem I PsaF

MacromoleculeName: Photosystem I PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 20.761107 KDa
SequenceString:
IDTAPVTKMK NLKTGTVEVD QTKLSVKSWG HMEPCGQNKK FQKRIKDEAF KLKKRQDKYA KGSAAYAGVQ EVIDQAKDTA KAYEGRWCG KKDGLPRVIA TGEVTRGGIV TPALMFLYTT GWIGYAGRSY LLRTKDAAKE IKIDVPLALT CMTSAFAWPV Y SWQDITNG RFVAKDTEIR VQRMHMA

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Macromolecule #7: Photosystem I PsaR

MacromoleculeName: Photosystem I PsaR / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 14.937079 KDa
SequenceString:
YTESAQDAKL FETVFSTYTA EYLKGPMYET PEKMIGRRPF NPGEPLWGED KKLTSNVLGP LKRVSSNELA FLTMICLAIG AWGEAQFLW FDPQFAAIDR GEYFNPIYII AASLLPVSFW AHIACYIQKA NGK

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Macromolecule #8: Photosystem I PsaI

MacromoleculeName: Photosystem I PsaI / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 14.184242 KDa
SequenceString:
AYGDGPKKWG AVLLPLTIFG VGITAMGTFV LYTFSEDFFW AFVPGSKRSM ELEKKKKEMA EKYPSPVVQH PADPLAGLVN RADYEKGLE EAWDKVKPKG STVTVEEKLK ELSTQNNPHY WRNAIKS

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Macromolecule #9: Photosystem I PsaJ

MacromoleculeName: Photosystem I PsaJ / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 7.757844 KDa
SequenceString:
RKIPAGPYSV SVEPLRDGAT NEVSIVTPPI SSEGVQEYLS LAPVFFMALA IFTSGFAIEV LRFFPDTRYW

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Macromolecule #10: Photosystem I PsaL

MacromoleculeName: Photosystem I PsaL / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 27.994172 KDa
SequenceString: VLPYMENIPR AIVEKEALEG VLAMTPREQW EDPPEDSVLY TLKVYAETYG EGKATKMPWW DWLYMRFELP DANEVSAEKI KLMEDDAKI QRRMMEGKIP LYVPILGVPI YTGMTLDWKP EAELFAGDQI RSPISDSRFA KNFIGNTAFY REGLENWQRG L EIGMAHGY ...String:
VLPYMENIPR AIVEKEALEG VLAMTPREQW EDPPEDSVLY TLKVYAETYG EGKATKMPWW DWLYMRFELP DANEVSAEKI KLMEDDAKI QRRMMEGKIP LYVPILGVPI YTGMTLDWKP EAELFAGDQI RSPISDSRFA KNFIGNTAFY REGLENWQRG L EIGMAHGY FLVGPFTTLG PLRNTPEAAT VGLLSACAVI GIVSVGGLLF GATVKPRAFD KDGATAGSGF TEIINWHAVG GL GGAGFCH LLLTLF

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Macromolecule #11: Photosystem I PsaM

MacromoleculeName: Photosystem I PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 9.634945 KDa
SequenceString:
ERIPGGKFTK AQGKIVATPD EDGFTDSEVA LALIIAAVVL YLAIEVTKSL FYGEDPETTA KGPMTPFEKR VVEKGLFGSR GDSYSPFRP

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Macromolecule #12: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 19.554451 KDa
SequenceString:
EFAGGLIGGQ SAFASQEYNF DPLGLAEKFP EQLPFFREAE LKHGRIAMLA WVGLVVPEFV RIPGPEKCWQ ASAVDAHSAC VETGALTQV FIFCGTLEIC GTWAKMNPMP YLPLSQSGST GGLTMENAGD YRLGVNFLPD EPEKVKEMKL KELKNGRLAM L AFGGAITQ ATLTGSGFPW LY

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Macromolecule #13: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 23.78017 KDa
SequenceString: AHPKHMLVAG VRGYEMEWQP IPGDAVKYPK PNSEEMFKTM IGADVETGGE AWDPLGFHKL FDRNFDFNML PVYPHVQWLR EAEIKHGRV CMLAFIGCFA QAGYHIGSYP VQPDWSKALA ECYASPTGAV GLFQISVLIG WIEGKNYNGD AWVGMSEKEP G DLGFDPAG ...String:
AHPKHMLVAG VRGYEMEWQP IPGDAVKYPK PNSEEMFKTM IGADVETGGE AWDPLGFHKL FDRNFDFNML PVYPHVQWLR EAEIKHGRV CMLAFIGCFA QAGYHIGSYP VQPDWSKALA ECYASPTGAV GLFQISVLIG WIEGKNYNGD AWVGMSEKEP G DLGFDPAG FTKNPDFDLK KAQLQEIKNG RLAMVGCASI AANHFIPGSV PLLTGFY

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Macromolecule #14: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 21.347398 KDa
SequenceString: KETSASVPFL PKPKNLAGWV GGETEFDPIG FSNWFDMKWL REAELKHGRV CMMATVGFVL QPYIGAYPGV EMPADSLQAV YAAPSEAWF AFIFAAGYIE SSSYNGKITQ LNMFEDSDRV PGNLGWGSTR LEGMSKEESE LMQLKELKNG RLAMLAFSGM V HHNIVVKG ...String:
KETSASVPFL PKPKNLAGWV GGETEFDPIG FSNWFDMKWL REAELKHGRV CMMATVGFVL QPYIGAYPGV EMPADSLQAV YAAPSEAWF AFIFAAGYIE SSSYNGKITQ LNMFEDSDRV PGNLGWGSTR LEGMSKEESE LMQLKELKNG RLAMLAFSGM V HHNIVVKG ALFPLVPDGW TGPEPWAVGS IMNNMG

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Macromolecule #15: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 19.171273 KDa
SequenceString:
GGYKMSKAVP FLPMSPALEG YVGAEEEGFD PMGFSLALDI RWLREAELKH GRICMLATVG WIATDLGMRL PGPAYQVSTL EAHDAMVKF GPMAQILIWL GIIEVFSFLA ITNMMEGTTD RQPGDYGLRR LYPKDEEGQY EMQLKELRNG RLAMLAFSGI V TTAVLTGR TWPF

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Macromolecule #16: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 19.33507 KDa
SequenceString:
FEGELGVTPP MGYFDPLGLS SDGDKKTFIR RRKSELKNGR VAMWACMGWI VPEWYRFPGE LSPSSGLKFS EIPNGMAALK ALPTEAWAQ MGAFVALLEL GPLWQDESRA PGDFKTCAKY GFPMFFVGGR EGSDSDPVKN QYSLNSEINN GRLAMMAITG M VFQNGITG TTGPEMWA

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Macromolecule #17: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 18.231799 KDa
SequenceString:
REAPKVLAGT GGPLPESFWD PAGFTNNKTD EELLFYRAAE LKHGRIAMAA VVGWFTNASG FHYLGDLWLK KPASDNPIEA FNQLSLLGV FQMVFFIGCL EWLTTVPCPP PKDAPWDVIG MSDVLEEDTD ENPMAEYKKI QMQELNNSRL AMVAIIGLIV Q ATTTG

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Macromolecule #18: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 18.956426 KDa
SequenceString:
FAGGLTGSDY GGFGGKYEWD PVGFSTRWPE HLAWYREAEL KHGRIAMLAF AGLLAPDLFR LPWAEFQDSS LDFANAHDKF VAGFGPMWW GFIACGGIEY QRFRKLGLGM EGLTLENAGN LGWFDLPKNS EERLFYETAE LKNGRLAMLA VSGIFTAGIF W DQHHFPFI

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Macromolecule #19: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5
type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 20.585494 KDa
SequenceString:
ARRELAVAYE DAGIDLMDNG KFAQGLVGAE AAFGRYEFDP IGFSKYTELV PWFREAELKH GRIAMLAWLG LVVPDFVRIP GEAYSFEAV PRVIDAHDAL NADAGPNFQI ILFISIVELC CAKKVFEWNS VETAGDYNLT RLFPEDDEAQ KQMRIAELKN G RLAMIAFG GAVTQAVITG KPFPWTF

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Macromolecule #20: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9
type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.068318 KDa
SequenceString:
FENELGVQAP TGFFDPLGLS SDGSIDNFKR RRASEIKHGR VAMLATMGYM TPEITGKFPG YLSYSQSIKF ADVPNGLAAM SKVPVLGWA QVAAYGAVCE LSQDQSPGTP GAAGDFGFKV ITSEDEETLK RKLNSELANG RLAMMAIIGL FFQDGLTGGA Y

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Macromolecule #21: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 19.562781 KDa
SequenceString:
VKMSPSVPYL PYPERLEGWV GGEKGFDPLR TSDIIDVYWL REAELKHGRI CMLATLGWIS VDAGWRFEAE MFQGVSVINA HNKMVEMGV MQQMLSIVGV CEIFSLYLIK EGLLGKIQRK AGDYFIGKNF LPKEEDKAKD MQLKELENGR LAMLAFSGIC T QANLFPES HFPY

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Macromolecule #22: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.109432 KDa
SequenceString:
FESELGVQAP TGFWDPLGFA KDGSMKAFKR RRASEIKHGR IAMLATMGYI TPEITGKFPG YLSPSTLLKY DDIPNGLGAI SKVPALGWA QIFVYCGYAE LSQDQTPGSP GAEGNFGFKV LTSSDPDSLE KKLASEIANG RLAMMAFTGM ATQDGLTGSA W

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Macromolecule #23: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13
type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.119342 KDa
SequenceString:
FENELGVQAP VGFWDPVGFT ADGNVASFRR RRTVELKHGR ISMLAAMGYM TPEITGKFPG YLSPSTLLKY DDIPNGLGAI SKVPALGWA QIFVYCGYAE LSQDQTPGSP GAEGNFGFKV LTSSDPDSLE KKLASEIANG RLAMMAFTGM ATQDGLTGSA W

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Macromolecule #24: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.422854 KDa
SequenceString:
ESERGAQPPF GFWDPLGLSA DGDVATFKRR RASEIKHGRI AMLAAMGYMT PEITGKFPGY LSPSTGVKYA DIPNGLAAIS KVPVVGWLQ IFAWTAVCEL WEDQVPGTPG HEGEFCFKAF KVTSDAPETR ETKLASELAN GRLAMMAIIG LFFQDGLTGS A Y

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Macromolecule #25: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16
type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.109498 KDa
SequenceString:
FESELGAQAP LGFFDPLKLT GDGSVEAFKR RRQSEIKHGR ISMLAAMGYM TPEITGKFPG YLSPSLNLKF ADVPNGLAAV SKVPAAGWA QILGYMAYCE TSQDQSAGTP GAAGEFGFKV ITSDDDEVLK RKLASELANG RLAMMAIIGM FYQDGLTGSA W

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Macromolecule #26: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17
type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.357012 KDa
SequenceString:
FENERGVQAP VGYWDPLGFA RDGNVALFKI RRATEIKHGR ISMLAAMGYI TPEVTGKFPG YLSPSMGLKF ADIPNGLAAI SKVPGYGWA QILGWMAFCE ISVDQSPGKP GAAGDMGFKA FKVTADAPET TEKKLASELA NGRLAMMAII GMFFQDGLTG S AW

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Macromolecule #27: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14
type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 17.355807 KDa
SequenceString:
FENELGVQAP TGFWDPLGFA KDGSMKAFKR RRASEIKHGR IAMLATMGYI TPELTGKFPG LLSPSMGLKY EDIPNGLGAI SKVPAVGWA QILAYTFYCE QSQDQSEGSA GEAGDFGFKV LTSKDEEGLK RKLNSELANG RLAMMAIIGM FFQDGLTGSA W

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Macromolecule #28: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1

MacromoleculeName: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1
type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Amphidinium carterae (eukaryote)
Molecular weightTheoretical: 15.280452 KDa
SequenceString:
VAGVCAPLTE KFDPLGLGTE EKMEQFTAAE IKHGRCAMIA CLGYVLPEWF RFPGCESYES GLGALGSLPA EGWFQLVALI GAHEVLVKP REGGLGAFDF GLGSELLEGQ SAEEVERKQT VERNNGRLAM VGFAGLVSQE LMF

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Macromolecule #29: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 29 / Number of copies: 223 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #30: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 30 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 31 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #32: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 32 / Number of copies: 12 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #33: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 33 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #34: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 34 / Number of copies: 11 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / 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 #36: (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: 36 / Number of copies: 49 / 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 / Diadinoxanthin

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Macromolecule #37: PERIDININ

MacromoleculeName: PERIDININ / type: ligand / ID: 37 / Number of copies: 49 / Formula: PID
Molecular weightTheoretical: 630.81 Da
Chemical component information

ChemComp-PID:
PERIDININ / Peridinin

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Macromolecule #38: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9...

MacromoleculeName: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0] ...Name: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
type: ligand / ID: 38 / Number of copies: 12 / Formula: UIX
Molecular weightTheoretical: 642.907 Da

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Macromolecule #39: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 39 / Number of copies: 39 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1 / Chlorophyll c

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Macromolecule #40: 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: 40 / Number of copies: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 356838
FSC plot (resolution estimation)

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