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- EMDB-4883: Structure of a minimal photosystem I from a green alga -

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Basic information

Entry
Database: EMDB / ID: EMD-4883
TitleStructure of a minimal photosystem I from a green alga
Map data
Sample
  • Complex: Photosystem I
    • Protein or peptide: x 11 types
  • Ligand: x 11 types
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / 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 / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / : / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB ...Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / : / 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: 3.2 Å
AuthorsPerez Boerema A / Klaiman D / Caspy I / Netzer-El SY / Amunts A / Nelson N
Funding support Israel, Sweden, 3 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
European Research CouncilERC-2018-StG-805230 Sweden
Swedish Research CouncilNT_2015-04107 Sweden
CitationJournal: Nat Plants / Year: 2020
Title: Structure of a minimal photosystem I from the green alga Dunaliella salina.
Authors: Annemarie Perez-Boerema / Daniel Klaiman / Ido Caspy / Sigal Y Netzer-El / Alexey Amunts / Nathan Nelson /
Abstract: Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular ...Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI.
History
DepositionApr 23, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseFeb 19, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rhz
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4883.png

Downloads & links

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Map

FileDownload / File: emd_4883.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1 / Movie #1: 1.5
Minimum - Maximum-4.307253 - 14.299224
Average (Standard dev.)0.010194603 (±0.18615824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.000426.000426.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-532-20
NX/NY/NZ1019393
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-4.30714.2990.010

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Supplemental data

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Mask #1

Fileemd_4883_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4883_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4883_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem I

EntireName: Photosystem I
Components
  • Complex: Photosystem I
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, Lhca2
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, 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: Photosystem I reaction center subunit II, PsaD
    • Protein or peptide: Photosystem I reaction center subunit IV, PsaE
    • Protein or peptide: Photosystem I reaction center subunit III, 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-CAROTENE
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Supramolecule #1: Photosystem I

SupramoleculeName: Photosystem I / 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: Chlorophyll a-b binding protein, Lhca2

MacromoleculeName: Chlorophyll a-b binding protein, 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: Chlorophyll a-b binding protein, Lhca4

MacromoleculeName: Chlorophyll a-b binding protein, 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: Photosystem I reaction center subunit II, PsaD

MacromoleculeName: Photosystem I reaction center subunit II, 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: Photosystem I reaction center subunit IV, PsaE

MacromoleculeName: Photosystem I reaction center subunit IV, 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: Photosystem I reaction center subunit III, PsaF

MacromoleculeName: Photosystem I reaction center subunit III, 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

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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

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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

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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

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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

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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

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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: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 19 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #22: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 22 / 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
Component:
ConcentrationFormulaName
3.0 mMC6H13NO5Tricine-Tris
0.05 %C22H42O10SB-DTM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 41.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, RELION (ver. 2.1)) / Number images used: 132017
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5l8r

RefinementSpace: REAL
Output model

PDB-6rhz:
Structure of a minimal photosystem I from a green alga

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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

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