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- EMDB-10995: Dunaliella Minimal Photosystem I -

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Basic information

Entry
Database: EMDB / ID: EMD-10995
TitleDunaliella Minimal Photosystem I
Map data
Sample
  • Complex: Large dunaliella salina photosystem I-LHC supercomplex
    • Protein or peptide: x 11 types
  • Ligand: x 12 types
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site ...Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2
Similarity search - Component
Biological speciesDunaliella salina (plant) / Green alga (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNelson N / Caspy I / Malavath T / Klaiman D / Shkolinsky Y
Funding support Israel, Belgium, 2 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
European Research Council (ERC)723991 Belgium
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.
Authors: Ido Caspy / Tirupathi Malavath / Daniel Klaiman / Maria Fadeeva / Yoel Shkolnisky / Nathan Nelson /
Abstract: Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained ...Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.
History
DepositionMay 3, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yxr
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10995.png

Downloads & links

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Map

FileDownload / File: emd_10995.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.067 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05646487 - 0.12832023
Average (Standard dev.)0.00011159403 (±0.0038285782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.12003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.120384.120384.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0560.1280.000

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Supplemental data

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Half map: #1

Fileemd_10995_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10995_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Large dunaliella salina photosystem I-LHC supercomplex

EntireName: Large dunaliella salina photosystem I-LHC supercomplex
Components
  • Complex: Large dunaliella salina photosystem I-LHC supercomplex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Lhca2
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Lhca4
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: Photosystem I reaction center subunit IX
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Large dunaliella salina photosystem I-LHC supercomplex

SupramoleculeName: Large dunaliella salina photosystem I-LHC supercomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Dunaliella salina (plant)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 21.30523 KDa
SequenceString: QRAGNFAPGS EPKEYLNDLP GNFNFDPLEL GKEKGTLQRY REAELIHCRW AMLGAAGCLA VEVLGLGNWY DAPLWAVTGD KPTWFGIEV PFDIATILGV EVVAMAVAEG LRNDNQDMEK RLYPGGAFDP LGFSKDPKSF EDKKLKELKN GRLAMVACLG F AGQHAATG ...String:
QRAGNFAPGS EPKEYLNDLP GNFNFDPLEL GKEKGTLQRY REAELIHCRW AMLGAAGCLA VEVLGLGNWY DAPLWAVTGD KPTWFGIEV PFDIATILGV EVVAMAVAEG LRNDNQDMEK RLYPGGAFDP LGFSKDPKSF EDKKLKELKN GRLAMVACLG F AGQHAATG KPILAALGDH LSSPFFNNFA TNGVSVPGV

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Macromolecule #2: Lhca2

MacromoleculeName: Lhca2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 22.813822 KDa
SequenceString: DRPLWSPGSE PPAWLDGSLA GDYGFDPLHL SEEPEMRKWM VQAELVHCRW AMLGVAGILF TSIGAKAGGN FPDWYDAGKE LQKNSDIPL GSLIFTELLL FGWVETKRLY DLRNPGSQGD GSFLGITDGL KGKENGYPGG LFDPMGMSKN EASFKEAKQK E VKNGRLAM ...String:
DRPLWSPGSE PPAWLDGSLA GDYGFDPLHL SEEPEMRKWM VQAELVHCRW AMLGVAGILF TSIGAKAGGN FPDWYDAGKE LQKNSDIPL GSLIFTELLL FGWVETKRLY DLRNPGSQGD GSFLGITDGL KGKENGYPGG LFDPMGMSKN EASFKEAKQK E VKNGRLAM LAFVGFIAQH HATHKSPIDN LLDHVADPFH VTFATNGVSI

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 22.732824 KDa
SequenceString: YLDGTLPGDY GFDPLGLLDP TVSNGQGAGG FVNPRWLQYS EVIHARWAML GAAGCIAPEI LGKAGVIPAE TAVDWFRTGV IPPAGVYKD FWADPFTLFF IEVVAIQFAE LKRLQDYKNP GSQSRQYFLG LEGLFKGSDN PAYPGGPFFN FANFGKTEAE M KKLKLNEI ...String:
YLDGTLPGDY GFDPLGLLDP TVSNGQGAGG FVNPRWLQYS EVIHARWAML GAAGCIAPEI LGKAGVIPAE TAVDWFRTGV IPPAGVYKD FWADPFTLFF IEVVAIQFAE LKRLQDYKNP GSQSRQYFLG LEGLFKGSDN PAYPGGPFFN FANFGKTEAE M KKLKLNEI KNGRLAMLAM FGYGAQAVIT GDGPFDNLLA HLADPTGANL IT

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Macromolecule #4: Lhca4

MacromoleculeName: Lhca4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 23.131031 KDa
SequenceString: DRPLWYPGAT PPAHLDGSML GDYGFDPLRL GTNPDRMKWF REAELTNGRW AMAAVVGILF TDVFTSIGLV GLPKWWEAGA QTYPIDNQT LRTLAIIEFL LFGWVETKRL YDLRNPGSQG DGSFLGITDG LKGTENGYPG GIFDPLGYSK TSPEKLDELQ N GRLAMLAF ...String:
DRPLWYPGAT PPAHLDGSML GDYGFDPLRL GTNPDRMKWF REAELTNGRW AMAAVVGILF TDVFTSIGLV GLPKWWEAGA QTYPIDNQT LRTLAIIEFL LFGWVETKRL YDLRNPGSQG DGSFLGITDG LKGTENGYPG GIFDPLGYSK TSPEKLDELQ N GRLAMLAF LGFASTAAVN GQGPIESLQT HLADPFHVTF ATNGVSIPHF TEF

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Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 81.748172 KDa
SequenceString: VKIAVDRNPV ETNFEKWAKP GHFSRALAKG PNTTTWIWNL HADAHDFDNH TSDLEEISRK VFSAHFGQLG IILIWLSGMY FHGARFSNY EGWLSDPTHI KPSAQVVWPI VGQEILNGDV GGGFQGIQIT SGFFQLWRAS GITSELQLYS TAIGGLVLAA A CFFAGWFH ...String:
VKIAVDRNPV ETNFEKWAKP GHFSRALAKG PNTTTWIWNL HADAHDFDNH TSDLEEISRK VFSAHFGQLG IILIWLSGMY FHGARFSNY EGWLSDPTHI KPSAQVVWPI VGQEILNGDV GGGFQGIQIT SGFFQLWRAS GITSELQLYS TAIGGLVLAA A CFFAGWFH YHKAAPKLEW FQNVESMLNH HLAGLLGLGS LAWAGHQIHV SLPVNKLLDA GVDPKEIPLP HEFLLNQSII AD LYPSFSK GLAPFFTLNW AEYSDFLTFK GGLNPVTGGL WLSDTAHHHL AIAVLFLVAG HQYRTNWGIG HSIKDILESH KGP FTGNGH AGLYEILTTS WHAQLAINLA LFGSLSIIVA HHMYAMPPYP YLATDYGTQL SLFTHHMWIG GFCVVGAGAH AAIF MVRDY DPTNNYNNLL DRVIRHRDAI ISHLNWVSIF LGFHSFGLYI HNDTMSALGR PQDMFSDTAI QLQPVFAQWI QNTHF TAPQ LTAPNALAAT SLTWGGDVVA VGGKVAMMPI ALGTSDFLVH HIHAFTIHVT VLILLKGVLF ARSSRLIPDK ANLGFR FPC DGPGRGGTCQ VSAWDHVFLG LFWMYNSLSI VIFHFSWKMQ SDVWGTVTDS GVSHITGGNF AQSANTINGW LRDFLWA QS SQVIQSYGSA LSAYGLMFLG AHFVWAFSLM FLFSGRGYWQ ELIESIVWAH NKLRVAPSIQ PRALSITQGR AVGVAHYL L GGIATTWSFF LARIIAVG

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 81.327992 KDa
SequenceString: FPKFSQGLAQ DPSTRRIWYG LATAHDFESH DGMTEENLYQ KIFASHFGQL AIIFLWTSGN LFHVAWQGNF EQWVTDPIHV RPIAHAIWD PHFGQPAVEA FTRGGASGPV NIATSGVYQW WYTIGLRSNQ ELYVSSVFLA LVSAVFLFAG WLHLQPNFQP S LSWFKDAE ...String:
FPKFSQGLAQ DPSTRRIWYG LATAHDFESH DGMTEENLYQ KIFASHFGQL AIIFLWTSGN LFHVAWQGNF EQWVTDPIHV RPIAHAIWD PHFGQPAVEA FTRGGASGPV NIATSGVYQW WYTIGLRSNQ ELYVSSVFLA LVSAVFLFAG WLHLQPNFQP S LSWFKDAE SRLNHHLAGL FGVSSLAWTG HLVHVAIPES RGQHVGWDNF LSVLPHPQGL TPFWSGNWAA YAQNPDTASH AF GTADGSG TAILTFLGGF HPQTQSLWLS DMAHHHLAIA VLFIVAGHMY RTNFGIGHRL EAILEAHTPP AGGLGAGHKG LFH TVNNSL HFQLGLALAS VGTITSLVAQ HMYSLPPYAY LAVDFTTQAS LYTHHQYIAG FIMCGAFAHG AIFFIRDYDP EQNK GNVLA RVLDHKEAII SHLSWVSLFL GFHTLGLYVH NDVVQAFGTP EKQILIEPVF AQWIQAAQGK SLYGFDLLLA SSSSP AYSA GQSLWLPGWL EAINNNQNSL FLTIGPGDFL VHHAIALGLH TTTLILVKGA LDARGSKLMP DKKDFGYSFP CDGPGR GGT CDISAYDAFY LAVFWMLNTI GWVTFYWHWK HLTLWQGNVS QFDESSTYLM GWLRDYLWLN SSQLINGYNP FGMNSLS VW AWTFLFGHLV YATGFMFLIS WRGYWQELIE TLVWAHEKTP LANLVYWKDK PVALSIVQAR LVGLAHFSVG YIFTYAAF L IASTAGRFG

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Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 8.71709 KDa
SequenceString:
AHVVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKAAQMAS SPRTEDCVGC KRCETACPTD FLSVRVYLGN ESTRSLGLAY

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Macromolecule #8: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 15.883294 KDa
SequenceString:
PWKQPELDPD TPSPIFGGST GGLLRKAQVE EFYVITWESP KEQIFEMPTG GAAIMRKGPN LLKFARKEQC MALTTQLRSK FRQTPCFYR VYADGKVQYL HPKDGVYPEK VNAGRVGVNQ NMRSIGKNVD PIKVVKFTGS EP

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Macromolecule #9: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 7.297158 KDa
SequenceString:
EIGPKRGSLV KVLRPESYWY NQVGKVVSVD QSGIRYPVVV RFENQNYAGV STNNYALDEI EEVK

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Macromolecule #10: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 18.212902 KDa
SequenceString:
DIAGLTPCSE SKAYNKLERK ELKVLDKRLK QYEPGSAPYL ALQATKERTE NRFKTYAKQG LLCGNDGLPH LISDPGLALR FNHAGEVFI PTFGFLYVAG YIGHVGRQYI ILSKEDAKPT DKEIILDVPL ALKLAFQGWA WPLASIQELR NGSLLEKDEN I TVS

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Macromolecule #11: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 4.467188 KDa
SequenceString:
MKDFTTYLST APVVGLGWAI FTSGLLIEIN RFFPDPLVFS

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Macromolecule #12: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 12 / Number of copies: 4 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Lutein

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Macromolecule #13: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 13 / Number of copies: 4 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Violaxanthin

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Macromolecule #14: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 14 / Number of copies: 23 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #15: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 134 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #16: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 16 / Number of copies: 10 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 17 / Number of copies: 6 / 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 #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 18 / Number of copies: 5 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #19: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 19 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

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Macromolecule #20: CHLOROPHYLL A ISOMER

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

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

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Macromolecule #21: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 21 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #22: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 22 / 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 #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 23 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: 2.5 sec blotting before plunging.

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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: 3.0 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4306 / Average electron dose: 42.68 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 720711
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rhz


Details: Minimal dunaliella salina photosystem I complex
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.7)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 45969
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6yxr:
Dunaliella Minimal Photosystem I

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About Yorodumi

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News

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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

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Aug 12, 2020. Covid-19 info

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