[English] 日本語
Yorodumi
- EMDB-36743: PSI-AcpPCI supercomplex from Symbiodinium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36743
TitlePSI-AcpPCI supercomplex from Symbiodinium
Map data
Sample
  • Complex: PSI-AcpPCI supercomplex from Symbiodinium
    • Protein or peptide: x 25 types
  • Ligand: x 12 types
KeywordsPhotosysrem I / Photosynthesis / Dinoflagellate
Function / homologyPhotosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / photosystem I / photosynthesis / membrane / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesSymbiodinium (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi XY / Li ZH / Wang WD
Funding support China, 9 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of Sciences2021YFA1300403 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 SciencesYSBR-004 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
DepositionJul 5, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_36743.png

Downloads & links

-
Map

FileDownload / File: emd_36743.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.215
Minimum - Maximum-0.31171027 - 1.6284502
Average (Standard dev.)0.0007149088 (±0.025184773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36743_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36743_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : PSI-AcpPCI supercomplex from Symbiodinium

EntireName: PSI-AcpPCI supercomplex from Symbiodinium
Components
  • Complex: PSI-AcpPCI supercomplex from Symbiodinium
    • 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: Photosystem I unk
    • Protein or peptide: Photosystem I unk
    • 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-10, acpPCI-10
    • 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: Photosystem I PsaA
    • Protein or peptide: Photosystem I PsaB
    • 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-9, acpPCI-9
    • 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-12, acpPCI-12
    • 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-5, acpPCI-5
    • 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-13, acpPCI-13
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • 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 A
  • Ligand: Chlorophyll c1Chlorophyll c
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PERIDININ
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

+
Supramolecule #1: PSI-AcpPCI supercomplex from Symbiodinium

SupramoleculeName: PSI-AcpPCI supercomplex from Symbiodinium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Symbiodinium (eukaryote)

+
Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 21.839982 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 IMNN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 19.596793 KDa
SequenceString: GGYKMSKAVP FLPMSPALEG YVGAEEEGFD PMGFSLALDI RWLREAELKH GRICMLATVG WIATDLGMRL PGPAYQVSTL EAHDAMVKF GPMAQILIWL GIIEVFSFLA ITNMMEGTTD RQPGDYGLRR LYPKDEEGQY EMQLKELRNG RLAMLAFSGI V TTAVLTGR ...String:
GGYKMSKAVP FLPMSPALEG YVGAEEEGFD PMGFSLALDI RWLREAELKH GRICMLATVG WIATDLGMRL PGPAYQVSTL EAHDAMVKF GPMAQILIWL GIIEVFSFLA ITNMMEGTTD RQPGDYGLRR LYPKDEEGQY EMQLKELRNG RLAMLAFSGI V TTAVLTGR TWPF(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #3: Photosystem I unk

MacromoleculeName: Photosystem I unk / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 6.656196 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #4: Photosystem I unk

MacromoleculeName: Photosystem I unk / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 11.166757 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 24.560145 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) HPKHMLVAGV RGYEMEWQPI PGDAVKYPKP NSEEMFKTM IGADVETGGE AWDPLGFHKL FDRNFDFNML PVYPHVQWLR EAEIKHGRVC MLAFIGCFAQ AGYHIGSYPV Q PDWSKALA ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) HPKHMLVAGV RGYEMEWQPI PGDAVKYPKP NSEEMFKTM IGADVETGGE AWDPLGFHKL FDRNFDFNML PVYPHVQWLR EAEIKHGRVC MLAFIGCFAQ AGYHIGSYPV Q PDWSKALA ECYASPTGAV GLFQISVLIG WIEGKNYNGD AWVGMSEKEP GDLGFDPAGF TKNPDFDLKK AQLQEIKNGR LA MVGCASI AANHFIPGSV PLLTGFY

+
Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 20.093357 KDa
SequenceString: EFAGGLIGGQ SAFASQEYNF DPLGLAEKFP EQLPFFREAE LKHGRIAMLA WVGLVVPEFV RIPGPEKCWQ ASAVDAHSAC V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK) ...String:
EFAGGLIGGQ SAFASQEYNF DPLGLAEKFP EQLPFFREAE LKHGRIAMLA WVGLVVPEFV RIPGPEKCWQ ASAVDAHSAC V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)GALTQVF IFCGTLEICG TWAKMNPM(UNK)(UNK) (UNK)GLTMENAGD YRLGVN FLP DEPEKVKEMK LKELKNGRLA MLAFGGAITQ ATLTGSGFPW LY

+
Macromolecule #7: Photosystem I PsaC

MacromoleculeName: Photosystem I PsaC / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 9.425731 KDa
SequenceString:
SHAVKIYDTC IGCTLCVRAC PTDVLEMVPA SINAAKQVAS SPRVEDCVGC KRCETACPTD FLSIRVYLQD NEETQYSLGL DLVDWS

+
Macromolecule #8: Photosystem I PsaD

MacromoleculeName: Photosystem I PsaD / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 24.878785 KDa
SequenceString: VVAEAIPRPE DLLDSPKFPM FEGSTGGYMS RSTRERHAIT WTAKGQAKFE MPTGGFAIMN QGENLCYFRK KEQCIALGKQ LRKMKIENY KIYRLKKDGT VIFMHPADGV FPEKVNKGRV QVNGRPFTIR GNPQQSELKF TKYQGKGYEA DPLTTMFVKA R VMAFADVP ...String:
VVAEAIPRPE DLLDSPKFPM FEGSTGGYMS RSTRERHAIT WTAKGQAKFE MPTGGFAIMN QGENLCYFRK KEQCIALGKQ LRKMKIENY KIYRLKKDGT VIFMHPADGV FPEKVNKGRV QVNGRPFTIR GNPQQSELKF TKYQGKGYEA DPLTTMFVKA R VMAFADVP NLFALPQPNM DELVPAEEVD KYTRQEYTTR MMEALKRVQD DRAAKAAKSL

+
Macromolecule #9: Photosystem I PsaE

MacromoleculeName: Photosystem I PsaE / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 8.266334 KDa
SequenceString:
PWVGPKKGSW VKILRPESYW FQQRGQVVNV NQKPEVKYPV TVKFDSVNYA NVNTNGYALW EVIEAPAPGP GEV

+
Macromolecule #10: Photosystem I PsaF

MacromoleculeName: Photosystem I PsaF / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 20.609658 KDa
SequenceString:
AKPLEMFGGV DIDLEDTPAH WTIKASPVLE PCKDNKKFHK KLKDELYKVK KNQQKFAEGS AAYARFNKKI KMIELRETAY GDRLCGKKD GLPRTIATGE WNVRGSAMWP AAIFLYIAGW IGWAGRSYLI RTNDAAKEIN IDVPLAVTCM ASGFSWPVAA W QEIVNGEM AVPNDQIHNG GPWNQS

+
Macromolecule #11: Photosystem I PsaR

MacromoleculeName: Photosystem I PsaR / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 15.221271 KDa
SequenceString:
YTETVADERL FEQVYLQYTS EYLKGPLYWH PDKLQGWLPD YPGTPMIKEG KYTSHVIGNL KAFSSNELAF LSMLFFGVGL YGNLQFNFY DPQWAKVDAG GFFNVSYIVE SFLLPISFFM HIACYIQRQN GK

UniProtKB: Uncharacterized protein

+
Macromolecule #12: Photosystem I PsaI

MacromoleculeName: Photosystem I PsaI / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 13.699559 KDa
SequenceString:
KYGDQRKFAA VLVPLTTLVF PAVAMGMFVL YSFQEDAFWR IVPGTKRARE LDEAWREHPL FANSKDPLDG LINPDDYEKG LEEAWERAK PAGSTVTVKD KLKQLSKQNN PHWESWRAMS

UniProtKB: Uncharacterized protein

+
Macromolecule #13: Photosystem I PsaJ

MacromoleculeName: Photosystem I PsaJ / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 11.153527 KDa
SequenceString:
AETEEGLIIK PEEAGKITSR DKNNNPPRIV VKTNDWDIPE YQLSTGASNQ VSYITPVVES EDIKAWLSLN VNFFSIIILF TVGGLIEIQ RFFPDTLYW

UniProtKB: Uncharacterized protein

+
Macromolecule #14: Photosystem I PsaL

MacromoleculeName: Photosystem I PsaL / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 27.708895 KDa
SequenceString: KIAYLQDIPR TIVEKDALEL ILKNTPKEQW ENPPEDSYLY TVKAFAEMYG PGKATKMGWW DYYRLKMDMP DTTRLSSERE LQEIEEYEK LMMSGKVPFA VPGPSGYFFT GFVTQWKGKE PFAGDQVITL TENGLFAKQF LSALAFYREG LKPWQRGLEI G MAHGYFLI ...String:
KIAYLQDIPR TIVEKDALEL ILKNTPKEQW ENPPEDSYLY TVKAFAEMYG PGKATKMGWW DYYRLKMDMP DTTRLSSERE LQEIEEYEK LMMSGKVPFA VPGPSGYFFT GFVTQWKGKE PFAGDQVITL TENGLFAKQF LSALAFYREG LKPWQRGLEI G MAHGYFLI GPFTSLGPLR NTPEAATVGL LCGCAIVGIV SIGGLIFGST IKPTRFDKDG DKPGAGFIEM INWHAVGGLG GA GFAHALI TVF

+
Macromolecule #15: Photosystem I PsaM

MacromoleculeName: Photosystem I PsaM / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 8.527976 KDa
SequenceString:
RVPGGKRTQE LGLVIPMADE DGLTDGQVAG LFVIALVVFI SAMDLAKTMY NGINPAKFKT SKGKGYISPL VKRYIENGF

UniProtKB: Uncharacterized protein

+
Macromolecule #16: Photosystem I PsaA

MacromoleculeName: Photosystem I PsaA / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 75.785336 KDa
SequenceString: IFRYINTTLW AKAGHFNKAL SKGAKTTTWI WNLHDYAHDF DIQQRSTGLI ARKVFSSNLA HLSLVFFWIS GMHLHGAYLS NYDIWLKDP KSITPSSHLA YSLIGQDILN SYTSEYFSGI TITSGFFQLY RSEGIITQSQ LKYACATSLI ATLICLSGSY L HMQLMSKF ...String:
IFRYINTTLW AKAGHFNKAL SKGAKTTTWI WNLHDYAHDF DIQQRSTGLI ARKVFSSNLA HLSLVFFWIS GMHLHGAYLS NYDIWLKDP KSITPSSHLA YSLIGQDILN SYTSEYFSGI TITSGFFQLY RSEGIITQSQ LKYACATSLI ATLICLSGSY L HMQLMSKF TSFYKKFQSL SQDHLIIIFG SRSTSLSAHQ IHKMLPANPL LDSGISKPSI LQVISNSLSY TLALFSTNLS ST GKLLNPS TRSVFLSQVA AHHKTTGVVF ITLGLIRFLT MYKSQFSILT SYIDYHIVLS INLALIASLS IIVADHLTRT PIY PHKSTS YPTILCLSIH HAWLSGFLII GSGAHASIFN LLGSPTSEIR HRDPIYSHLI WVCIAIGLHS FSLYCHNDTL EALG RPEDI FHDNSIQLKA IFAKQSFLRA ELQPDIEMLD KKIIRITQEL GTADFIVHHI HAFTIHVTLL ILSKGVLYAR NSRFV SDKL ELGFTYPCDG PGRGGTCQIS PWDHLFSAVF WMYNCLNVVT FHYFWKMQSD VWGFVSIQKH ISHYSQGDFS VNSITI NGW LRNLLWSEAS QVIQSYALSS ICPYGFIFLI GHFIWAFSLM FLFSGRAYWQ ELIESILWSH HKLKIIPHIQ PRALSIS QG RAVGFIHYTL GGIGSTWAFI ISRLLVLT

+
Macromolecule #17: Photosystem I PsaB

MacromoleculeName: Photosystem I PsaB / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 74.438906 KDa
SequenceString: GRCASSRYLQ VLGSIHDIEC GFGIDNTLSL NLQIFTAHWG HLTIILIWVS SNLYHIASNA NYSLWVKNPI PSMPIAHNIW DPHFTNSTS TPYSHTIITT ILIAYSGIYN QLYTSGFNTI NQIYKTTFTF SCLAVISILL AKIHINTHSE LLHKLASHTS Q IPSFFQLL ...String:
GRCASSRYLQ VLGSIHDIEC GFGIDNTLSL NLQIFTAHWG HLTIILIWVS SNLYHIASNA NYSLWVKNPI PSMPIAHNIW DPHFTNSTS TPYSHTIITT ILIAYSGIYN QLYTSGFNTI NQIYKTTFTF SCLAVISILL AKIHINTHSE LLHKLASHTS Q IPSFFQLL YFLDVAISSV NIRFNFHTGI LVGLFSIGYT GHLLDITIPA SRAPLIHTSP SYLTFFGGLK SNTSSLYLTD IA HHHLAIG IISILTGHLY SSFRAALGTY IRDILYTSHL THSIKSLHLA LSLILASCTP LTSTTAQHIY SLTPYFYLSY DHI YSTALY VHHSYITSFL AIASHAHTAI TLVRDWVAPL EQESSSKQIR IHTHKAAIIS HLSWVSLWLG FHTLAVYSHN DTCI AFNSP SKQILIEASN GQLIQQASGK ALYGTINSIN NYNKSFDSFI HPISPGDLYV HHAIALGLHI TVLILLKGGL EARGS KLMP DKMEHSFGFS CDGPGRGGTC DISAWDSFYL ATFWMLNSNA WISFYFHYKH LTPRQFSESS TYLESWFRDY LWFNST PLI HGYSTLGAND LSVQSWSFLL THLAWASGFM FLISWRGYWQ ELIDIILYIH LKTPILINLW NGDIYTPLAL SIVQARF IG LVHFSTGLIL TYPPFIIGAT S

+
Macromolecule #18: 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: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 21.264883 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)VKMSPSVPY LPYPERLEGW VGGEKGFDPL RTSDIIDVYW LREAELKHGR ICMLATLGWI S VDAGWRFE AEMFQGVSVI ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)VKMSPSVPY LPYPERLEGW VGGEKGFDPL RTSDIIDVYW LREAELKHGR ICMLATLGWI S VDAGWRFE AEMFQGVSVI NAHNKMVEMG VMQQMLSIVG VCEIFSLYLI KEGLLGKIQR KAGDYFIGKN FLPKEEDKAK DM QLKELEN GRLAMLAFSG ICTQANLFPE SHFPY

+
Macromolecule #19: 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: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 17.493844 KDa
SequenceString:
FENELGVQAP TGFFDPLGLS SDGSIDNFKR RRASEIKHGR VAMLATMGYM TPEITGKFPG YLSYSQSIKF ADVPNGLAAM SKVPVLGWA QVAAYGAVCE LSQDQSPGTP GAAGDFGF(UNK)(UNK) (UNK)(UNK)(UNK)KVITSED EETLKRKLNS E LANGRLAM MAIIGLFFQD GLTGGAY

+
Macromolecule #20: 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: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (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

+
Macromolecule #21: 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: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 17.109432 KDa
SequenceString:
FESELGVQAP TGFWDPLGFA KDGSMKAFKR RRASEIKHGR IAMLATMGYI TPEITGKFPG YLSPSTLLKY DDIPNGLGAI SKVPALGWA QIFVYCGYAE LSQDQTPGSP GAEGNFGFKV LTSSDPDSLE KKLASEIANG RLAMMAFTGM ATQDGLTGSA W

+
Macromolecule #22: 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: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 22.912516 KDa
SequenceString: REAPKVLAGT GGPLPESFWD PAGFTNNKTD EELLFYRAAE LKHGRIAMAA VVGWFTNASG FHYLGDLWLK KPASDNPIEA FNQLSLLGV FQMVFFIGCL EWLTTVPCPP PKDAPWDVIG MSDVLEEDTD ENPMAEYKKI QMQELNNSRL AMVAIIGLIV Q ATTTG(UNK) ...String:
REAPKVLAGT GGPLPESFWD PAGFTNNKTD EELLFYRAAE LKHGRIAMAA VVGWFTNASG FHYLGDLWLK KPASDNPIEA FNQLSLLGV FQMVFFIGCL EWLTTVPCPP PKDAPWDVIG MSDVLEEDTD ENPMAEYKKI QMQELNNSRL AMVAIIGLIV Q ATTTG(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #23: 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: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (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

+
Macromolecule #24: 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: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 19.381953 KDa
SequenceString:
FAGGLTGSDY GGFGGKYEWD PVGFSTRWPE HLAWYREAEL KHGRIAMLAF AGLLAPDLFR LPWAEFQDSS LDFANAHDKF VAG(UNK)(UNK)(UNK)(UNK)(UNK)F GPMWWGFIAC GGIEYQRFRK LGLGMEGLTL ENAGNLGWFD LPKNSEERLF Y ETAELKNG RLAMLAVSGI FTAGIFWDQH HFPFI

+
Macromolecule #25: 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: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Symbiodinium (eukaryote)
Molecular weightTheoretical: 17.119342 KDa
SequenceString:
FENELGVQAP VGFWDPVGFT ADGNVASFRR RRTVELKHGR ISMLAAMGYM TPEITGKFPG YLSPSTLLKY DDIPNGLGAI SKVPALGWA QIFVYCGYAE LSQDQTPGSP GAEGNFGFKV LTSSDPDSLE KKLASEIANG RLAMMAFTGM ATQDGLTGSA W

+
Macromolecule #26: (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: 26 / Number of copies: 41 / 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

+
Macromolecule #27: [(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: 27 / Number of copies: 7 / Formula: UIX
Molecular weightTheoretical: 642.907 Da

+
Macromolecule #28: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 28 / Number of copies: 189 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #29: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 29 / Number of copies: 20 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1 / Chlorophyll c

+
Macromolecule #30: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 30 / Number of copies: 7 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #31: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 31 / Number of copies: 9 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #32: PERIDININ

MacromoleculeName: PERIDININ / type: ligand / ID: 32 / Number of copies: 18 / Formula: PID
Molecular weightTheoretical: 630.81 Da
Chemical component information

ChemComp-PID:
PERIDININ / Peridinin

+
Macromolecule #33: 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: 33 / Number of copies: 1 / 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

+
Macromolecule #34: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 34 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #35: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 35 / Number of copies: 12 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #36: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 36 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #37: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 37 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216895
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more