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- EMDB-10236: Dunaliella Photosystem I Supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-10236
TitleDunaliella Photosystem I Supercomplex
Map data
Sample
  • Complex: Large dunaliella salina photosystem I-LHC supercomplex
    • Protein or peptide: x 19 types
  • Ligand: x 20 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: 2.84 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
DepositionAug 18, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseJun 24, 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: 0.0247
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0247
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sl5
  • Surface level: 0.0247
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10236.png

Downloads & links

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Map

FileDownload / File: emd_10236.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: 0.0247 / Movie #1: 0.0247
Minimum - Maximum-0.07073394 - 0.15494287
Average (Standard dev.)0.00016259018 (±0.005252027)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0710.1550.000

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Supplemental data

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Half map: #1

Fileemd_10236_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_10236_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: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PsaG
    • Protein or peptide: PsaH
    • Protein or peptide: PsaI
    • Protein or peptide: PsaK
    • Protein or peptide: PsaL
    • Protein or peptide: PsaO
    • 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: Lhca5
    • Protein or peptide: Lhca6
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: octadecanal
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Tripalmitoylglycerol
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • 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: CHLOROPHYLL B
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
  • Ligand: [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate

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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-#19
Source (natural)Organism: Dunaliella salina (plant)

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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: Green alga (plant)
Molecular weightTheoretical: 81.877352 KDa
SequenceString: KVKIAVDRNP VETNFEKWAK PGHFSRALAK GPNTTTWIWN LHADAHDFDN HTSDLEEISR KVFSAHFGQL GIILIWLSGM YFHGARFSN YEGWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY STAIGGLVLA A ACFFAGWF ...String:
KVKIAVDRNP VETNFEKWAK PGHFSRALAK GPNTTTWIWN LHADAHDFDN HTSDLEEISR KVFSAHFGQL GIILIWLSGM YFHGARFSN YEGWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY STAIGGLVLA A ACFFAGWF HYHKAAPKLE WFQNVESMLN HHLAGLLGLG SLAWAGHQIH VSLPVNKLLD AGVDPKEIPL PHEFLLNQSI IA DLYPSFS KGLAPFFTLN WAEYSDFLTF KGGLNPVTGG LWLSDTAHHH LAIAVLFLVA GHQYRTNWGI GHSIKDILES HKG PFTGNG HAGLYEILTT SWHAQLAINL ALFGSLSIIV AHHMYAMPPY PYLATDYGTQ LSLFTHHMWI GGFCVVGAGA HAAI FMVRD YDPTNNYNNL LDRVIRHRDA IISHLNWVSI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPVFAQW IQNTH FTAP QLTAPNALAA TSLTWGGDVV AVGGKVAMMP IALGTSDFLV HHIHAFTIHV TVLILLKGVL FARSSRLIPD KANLGF RFP CDGPGRGGTC QVSAWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVTD SGVSHITGGN FAQSANTING WLRDFLW AQ SSQVIQSYGS ALSAYGLMFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLRVAPSI QPRALSITQG RAVGVAHY L LGGIATTWSF FLARIIAVG

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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: Green alga (plant)
Molecular weightTheoretical: 81.671438 KDa
SequenceString: TKLFPKFSQG LAQDPSTRRI WYGLATAHDF ESHDGMTEEN LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEQWVTDP IHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIATSGV YQWWYTIGLR SNQELYVSSV FLALVSAVFL FAGWLHLQPN F QPSLSWFK ...String:
TKLFPKFSQG LAQDPSTRRI WYGLATAHDF ESHDGMTEEN LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEQWVTDP IHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIATSGV YQWWYTIGLR SNQELYVSSV FLALVSAVFL FAGWLHLQPN F QPSLSWFK DAESRLNHHL AGLFGVSSLA WTGHLVHVAI PESRGQHVGW DNFLSVLPHP QGLTPFWSGN WAAYAQNPDT AS HAFGTAD GSGTAILTFL GGFHPQTQSL WLSDMAHHHL AIAVLFIVAG HMYRTNFGIG HRLEAILEAH TPPAGGLGAG HKG LFHTVN NSLHFQLGLA LASVGTITSL VAQHMYSLPP YAYLAVDFTT QASLYTHHQY IAGFIMCGAF AHGAIFFIRD YDPE QNKGN VLARVLDHKE AIISHLSWVS LFLGFHTLGL YVHNDVVQAF GTPEKQILIE PVFAQWIQAA QGKSLYGFDL LLASS SSPA YSAGQSLWLP GWLEAINNNQ NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAYD AFYLAVFWML NTIGWVTFYW HWKHLTLWQG NVSQFDESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWTFLFG HLVYATGFMF LISWRGYWQE LIETLVWAHE KTPLANLVYW KDKPVALSIV QARLVGLAHF SVGYIFTY A AFLIASTAGR FG

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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: Green alga (plant)
Molecular weightTheoretical: 8.71709 KDa
SequenceString:
AHVVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKAAQMAS SPRTEDCVGC KRCETACPTD FLSVRVYLGN ESTRSLGLAY

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Macromolecule #4: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 16.214705 KDa
SequenceString:
PWKQPELDPD TPSPIFGGST GGLLRKAQVE EFYVITWESP KEQIFEMPTG GAAIMRKGPN LLKFARKEQC MALTTQLRSK FRQTPCFYR VYADGKVQYL HPKDGVYPEK VNAGRVGVNQ NMRSIGKNVD PIKVVKFTGS APFEI

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Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / 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 #6: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 18.115789 KDa
SequenceString:
DIAGLTPCSE SKAYNKLERK ELKVLDKRLK QYEPGSAPYL ALQATKERTE NRFKTYAKQG LLCGNDGLPH LISDPGLALR FNHAGEVFI TFGFLYVAGY IGHVGRQYII LSKEDAKPTD KEIILDVPLA LKLAFQGWAW PLASIQELRN GSLLEKDENI T VS

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Macromolecule #7: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Green alga (plant)
Molecular weightTheoretical: 4.614362 KDa
SequenceString:
MKDFTTYLST APVVGLGWAI FTSGLLIEIN RFFPDPLVFS F

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Macromolecule #8: PsaG

MacromoleculeName: PsaG / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 10.928419 KDa
SequenceString:
LEPAVAIGGS TVSFLALGRF VFLPYQRRRT EMEVGPGRLG PKTTGDTFFD RLQKPASFVE TKSKDPSGFG GWHAALGHVF GYFLLACSS LQDAGQVIAH WG

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Macromolecule #9: PsaH

MacromoleculeName: PsaH / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 10.012247 KDa
SequenceString:
KYFDVQDLEN TTGAWDLYGV DEMKRYPGLQ EEFFQRATDA VSRREALNGF VALSAGVASI ALFGKGASTL ELPIGTKGPR MEKTENGKG GIL

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Macromolecule #10: PsaI

MacromoleculeName: PsaI / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 4.236944 KDa
SequenceString:
ATEGYPFVPP DWAPALFVPL TGLVLPAVGM AWAFTYIQK

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Macromolecule #11: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 8.191218 KDa
SequenceString:
GQSGSVRAIM VSSIGACLFA SRFGLAPSVR KNATAAGTDL EKSVHAAGDD PGAGFTATDV LAMGAAGHAI GVGEWLAQLA RGGV

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Macromolecule #12: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 16.189839 KDa
SequenceString:
QQVIQPLNGD PFVGMLETPV TSAPIVANYL SNLPAYRTGV APNLRGVEIG LAHGFLLAGP FIKLGPLRDV PGTAEVVGCM SAALVLILA LCLSLYGNAA FQNQPSMGKK TLSGRPLPQD PLMSEEGWAK FAAGFTVGGL SGVAWAYILT QVCLGR

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Macromolecule #13: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 9.635004 KDa
SequenceString:
LRVDPIVPAI SFVGWTLPSN IGTSALNGQS LFGAFYESIG QNLAHWPTGF ALDDKFWLYM VTWHTGLFIV MLLGQVGFKG RTEDYF

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Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / 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 #15: Lhca2

MacromoleculeName: Lhca2 / type: protein_or_peptide / ID: 15 / 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 #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 24.58591 KDa
SequenceString: SKDFLYVGSD AAALKYLDGT LPGDYGFDPL GLLDPTVSNG QGAGGFVNPR WLQYSEVIHA RWAMLGAAGC IAPEILGKAG VIPAETAVD WFRTGVIPPA GVYKDFWADP FTLFFIEVVA IQFAELKRLQ DYKNPGSQSR QYFLGLEGLF KGSDNPAYPG G PFFNFANF ...String:
SKDFLYVGSD AAALKYLDGT LPGDYGFDPL GLLDPTVSNG QGAGGFVNPR WLQYSEVIHA RWAMLGAAGC IAPEILGKAG VIPAETAVD WFRTGVIPPA GVYKDFWADP FTLFFIEVVA IQFAELKRLQ DYKNPGSQSR QYFLGLEGLF KGSDNPAYPG G PFFNFANF GKTEAEMKKL KLNEIKNGRL AMLAMFGYGA QAVITGDGPF DNLLAHLADP TGANLITNLG

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Macromolecule #17: Lhca4

MacromoleculeName: Lhca4 / type: protein_or_peptide / ID: 17 / 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 #18: Lhca5

MacromoleculeName: Lhca5 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 21.676771 KDa
SequenceString: LPAIPLADVQ SLSYLDGHLP GDMGFDPLHL GSGVLSQDWL RYAEVVHGRW AMLGVVGCLT PEALAMRGTI PPERGVEDNQ TLLIIEIAV FSFLESKRYE GYKKTGEGGF INSYPFDPVG LNSPKHAVNE LQQNGRLAML AFLGFASTAA VNGQGPIESL Q THIADPAH ...String:
LPAIPLADVQ SLSYLDGHLP GDMGFDPLHL GSGVLSQDWL RYAEVVHGRW AMLGVVGCLT PEALAMRGTI PPERGVEDNQ TLLIIEIAV FSFLESKRYE GYKKTGEGGF INSYPFDPVG LNSPKHAVNE LQQNGRLAML AFLGFASTAA VNGQGPIESL Q THIADPAH NNVFTSSVGK ESCVFVAVLS ILPMLIEANK ALGK

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Macromolecule #19: Lhca6

MacromoleculeName: Lhca6 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dunaliella salina (plant)
Molecular weightTheoretical: 19.559611 KDa
SequenceString:
LPDVIPPPHL NGTLPGDSFD PLGLGLNEER LKWSVTMGKT NCRWAMMAVT GIMGQELLGV PVKWFEAGAA EYDLPVQAQV PILFLVMGF LETKRFQGFR ESGFINSYPF DPVGLNSPKH ATKEVKNGRL AMVAFVGFAV QALVTRTQPI EGLQKHLADP F GKNITYYL THTPEVIAGT

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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: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 172 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #22: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 22 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #23: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 23 / 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 #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 31 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #25: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 25 / Number of copies: 15 / 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 #26: octadecanal

MacromoleculeName: octadecanal / type: ligand / ID: 26 / Number of copies: 1 / Formula: OCD
Molecular weightTheoretical: 268.478 Da
Chemical component information

ChemComp-OCD:
octadecanal / Octadecanal

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Macromolecule #27: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 27 / Number of copies: 4 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #29: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 29 / Number of copies: 4 / 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 #30: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 31 / Number of copies: 8 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #32: Tripalmitoylglycerol

MacromoleculeName: Tripalmitoylglycerol / type: ligand / ID: 32 / Number of copies: 2 / Formula: 4RF
Molecular weightTheoretical: 807.32 Da
Chemical component information

ChemComp-4RF:
Tripalmitoylglycerol / Tripalmitin

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Macromolecule #33: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 33 / Number of copies: 9 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #34: (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: 34 / Number of copies: 9 / 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 #35: (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: 35 / Number of copies: 6 / 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 #36: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 36 / Number of copies: 13 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #37: 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: 37 / Number of copies: 3 / 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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Macromolecule #38: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S...

MacromoleculeName: trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
type: ligand / ID: 38 / Number of copies: 2 / Formula: LMK
Molecular weightTheoretical: 773.241 Da
Chemical component information

ChemComp-LMK:
trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium

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Macromolecule #39: [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3...

MacromoleculeName: [(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate
type: ligand / ID: 39 / Number of copies: 2 / Formula: P3H
Molecular weightTheoretical: 722.841 Da
Chemical component information

ChemComp-P3H:
[(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
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)
Final 3D classificationNumber classes: 12 / Avg.num./class: 27366 / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 189006
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 83
Output model

PDB-6sl5:
Dunaliella Photosystem I Supercomplex

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