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- EMDB-0821: PSI-LHCI Supercomplex from Physcometrella patens -

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Basic information

Entry
Database: EMDB / ID: EMD-0821
TitlePSI-LHCI Supercomplex from Physcometrella patens
Map data
Sample
  • Complex: PSI-LHCI
  • Protein or peptide: x 17 types
  • Ligand: x 10 types
Function / homology
Function and homology information


photosystem I antenna complex / response to low light intensity stimulus / pigment binding / response to high light intensity / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : ...photosystem I antenna complex / response to low light intensity stimulus / pigment binding / response to high light intensity / photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / serine-type endopeptidase activity / magnesium ion binding / protein homodimerization activity / metal ion binding
Similarity search - Function
: / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) ...: / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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. / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 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
PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / PSI-F / Photosystem I reaction center subunit V, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K ...PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / PSI-F / Photosystem I reaction center subunit V, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / PSI subunit V / Predicted protein / Photosystem I reaction center subunit V, chloroplastic / PsaH photosystem I reaction center subunit / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesPhyscomitrella patens (plant) / Moss (plant)
Methodsingle particle reconstruction / Resolution: 3.23 Å
AuthorsZhao L / Yan QJ / Qin XC
CitationJournal: Cell Discov / Year: 2021
Title: Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens.
Authors: Qiujing Yan / Liang Zhao / Wenda Wang / Xiong Pi / Guangye Han / Jie Wang / Lingpeng Cheng / Yi-Kun He / Tingyun Kuang / Xiaochun Qin / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of ...Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 Å resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing.
History
DepositionOct 9, 2019-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l35
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0821.png

Downloads & links

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Map

FileDownload / File: emd_0821.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05337422 - 0.16238572
Average (Standard dev.)8.22962e-05 (±0.0043891533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z407.424407.424407.424
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0530.1620.000

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Supplemental data

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Sample components

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Entire : PSI-LHCI

EntireName: PSI-LHCI
Components
  • Complex: PSI-LHCI
  • 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: Predicted protein PsaDPrediction
  • Protein or peptide: PsaE
  • Protein or peptide: PSI-F
  • Protein or peptide: Predicted protein PsaGPrediction
  • Protein or peptide: PsaH photosystem I reaction center subunit
  • Protein or peptide: Photosystem I reaction center subunit VIII
  • Protein or peptide: Photosystem I reaction center subunit IX
  • Protein or peptide: PsaK
  • Protein or peptide: PSI subunit V
  • Protein or peptide: Photosystem I reaction center subunit XII
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL B
  • 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

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Supramolecule #1: PSI-LHCI

SupramoleculeName: PSI-LHCI / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Physcomitrella patens (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: Moss (plant)
Molecular weightTheoretical: 82.313422 KDa
SequenceString: EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF ...String:
EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF HYHKAAPKLA WFQNVESMLN HHLAGLLGLG SLAWAGHQVH VSLPINRLLD AGVDPKEIPL PHEFILNRDL LA QLYPSFS KGLTPFFTLN WSEYSDFLTF RGGLNPVTGG LWLTDTAHHH LAIAVLFLVA GHMYRTNFGI GHSMKEILEA HKG PFTGEG HKGLYEILTT SWHAQLAINL AMLGSLTIIV AHHMYAMPPY PYLATDYATQ LSLFTHHMWI GGFLVVGAAA HAAI FMVRD YDPTTQYNNL LDRVLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPVFAQW IQNTH ALAP SLTAPNATAS TSLTWGGGDL VAVGGKVALL PIPLGTADFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNAI SVVIFHFSWK MQSDVWGSIS DQGVVTHITG GNFAQSSITI NGWLRDF LW AQASQVIQSY GSSLSAYGLL FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALSIV QGRAVGVA H YLLGGIATTW AFFLARIISV G

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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: Moss (plant)
Molecular weightTheoretical: 82.316547 KDa
SequenceString: ASRFPKFSRG LSQDPTTRRI WFGIATAHDF ESHDDMTEER LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWGQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIAYSGV YQWWYTIGLR TNQDLYGGSI FLLFVSALFL IAGWLHLQPK W KPSVSWFK ...String:
ASRFPKFSRG LSQDPTTRRI WFGIATAHDF ESHDDMTEER LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWGQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIAYSGV YQWWYTIGLR TNQDLYGGSI FLLFVSALFL IAGWLHLQPK W KPSVSWFK NAESRLNHHL SGLFGVSSLA WTGHLVHVAI PESRGEHVRW NNLLTALPHP QGLGPFFAGQ WNVYAQNPDS NS HLFGTSE GAGTAILTFL GGFHPQTQSL WLTDMAHHHL AIAVIFIIAG HMYRTNFGIG HSMKEILEAH TPPGGRLGRG HKG LYDTIN NSLHFQLGLA LASLGVITSL VAQHMYSLPP YAFLAQDFTT QAALYTHHQY IAGFIMTGAF AHGAIFFIRD YNPE QNKDN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YVHNDVMLAF GTPEKQILIE PVFAQWIQSA HGKALYGFDV LLSSA DSPA FNAGQTLWLP GWLDAINNNS NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKEFGY SFPCDG PGR GGTCDISAWD AFYLAVFWML NTIGWVTFYW HWKHITLWQG NVAQFNESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWMFLFG HLVWATGFMF LISWRGYWQE LIETLAWAHE RTPLANLVRW KDKPVALSIV QARLVGLAHF SVGYIFTY A AFLIASTSGK 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: Moss (plant)
Molecular weightTheoretical: 8.649957 KDa
SequenceString:
AHSVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKASQIAS APRTEDCVGC KRCESACPTD FLSVRVYLGA ETTRSMGLAY

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Macromolecule #4: Predicted protein PsaD

MacromoleculeName: Predicted protein PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 15.654927 KDa
SequenceString:
TPPTLNADTP APIFGGSTGG LLRKAQVEEF YVITWESPKE QIFEMPTGGA AIMRSGPNLL KLARKEQCLA LGARLRTKFK IQYQFYRVF PNGEVQYLHP KDGVYPEKVN AGRSPVGVNN RSIGKNANPA ELKFAHKQAY DL

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Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 6.895725 KDa
SequenceString:
GPKRGSIVKV LRRESYWFND TGKVVAVDQA PGVRYPVVVR FDKVNYAGVS TNNYSPDELE AA

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Macromolecule #6: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 17.465363 KDa
SequenceString:
DVAGLTPCKE SKGFAKREKQ EIKKLESRLK LYAPDSAPAL ALNATIEKTK RRFAFYGNEG LLCGTDGLPH LIVDGDQAHL GEFVYPGLV FLYIAGWIGW VGRAYLIDVR TSKKPTEKEI IIDVPLALRI MSKGLTWPVA AIGELRSGKL VEKSANITVS

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Macromolecule #7: Predicted protein PsaG

MacromoleculeName: Predicted protein PsaG / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 10.564831 KDa
SequenceString:
EANTALTITL STGALLFLGR FVFLPFQRDN VSRQGLPVQN GVTHFDAGDS RAQEVTSFLK TNDPAGFTIV DVLAWGALGH AVGFFILAT INNGYNPQF

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Macromolecule #8: PsaH photosystem I reaction center subunit

MacromoleculeName: PsaH photosystem I reaction center subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 9.861088 KDa
SequenceString:
SVYFDLGEID NTTGNWDLYG NDDPNRYNGF QNKFFETFAG AFTKRGLLLK FLVLGGATTI GYLGSTSSPD LLAIKNGPKQ VPVMGPRGR K

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Macromolecule #9: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 3.791472 KDa
SequenceString:
MTASYLPSIF VPLIGLVFPA ITMASLFIYI EQDE

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Macromolecule #10: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 4.59746 KDa
SequenceString:
MQDVKTYLST APVLATLWFG FLAGLLIEIN RFFPDALVLP L

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Macromolecule #11: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 7.916146 KDa
SequenceString:
YIGSSTNLIM VASTTLMLFA GRFGLAPSAN RKSTAGLKLV DRDSGLQTGD PAGFTATDTL ACGALGHVIG VGIVLGLKA

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Macromolecule #12: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 16.892416 KDa
SequenceString:
KYQVIEPLNG DPFIGGFETP VTSSPLIAWY LSNLPAYRTA VAPLLRGVEI GLAHGYLLVG PFVLTGPLRN SAVRGEAGSL AAAGLVTIL TMCLTIYGIA SFKEGEPSKA PSLTLTGRQK DADKLQTAEG WASFTGGWFF GGLSGVAWAY ILLYVLNLPY

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Macromolecule #13: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 3.051623 KDa
SequenceString:
SISDSQIIVA LVSAFITGIL ALRLGKSLY

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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: Moss (plant)
Molecular weightTheoretical: 22.922107 KDa
SequenceString: ALPNNDRPLW FPGSKAPEWL DGSLPGDFGF DPLGLGSDPE LLKWFVQAEL VHCRWAMLGA AGIFIPEALT KAGILNTPSW NVAGDQQYF ADPTTLFVIE LILFAWAEGR RWADIVNPGC VNVDPVFPNN KLTGTDVGYP GGLWFDPLGW GQTKDAKKLK E LRTKEIKN ...String:
ALPNNDRPLW FPGSKAPEWL DGSLPGDFGF DPLGLGSDPE LLKWFVQAEL VHCRWAMLGA AGIFIPEALT KAGILNTPSW NVAGDQQYF ADPTTLFVIE LILFAWAEGR RWADIVNPGC VNVDPVFPNN KLTGTDVGYP GGLWFDPLGW GQTKDAKKLK E LRTKEIKN GRLAMLAVLG AVVQANYTHT GPIDNLLAHL ADPGHNTIFA LS

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 20.761584 KDa
SequenceString: EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPVILAIE FLAIAFAESQ RNGEPDPEKR KYPGGAFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFA V QAIAYPGT ...String:
EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AVPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPVILAIE FLAIAFAESQ RNGEPDPEKR KYPGGAFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFA V QAIAYPGT GPLENLKTHL ADPWHNTIAH VIIP

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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: Moss (plant)
Molecular weightTheoretical: 23.250502 KDa
SequenceString: FASKQSLSYL DGTLPGDYGF DPLGLMDPEG AGGFIDPQWL PYAEIINGRF AMLGAAGAIA PEVLGRIGLI PQETAIPWFQ SGVIPPVGN YSYWADPYTL FVLEMALMGF AEHRRAQDYY KPGSMGKQYF LGLEKFLGGS GNPAYPGGPI FNFLGFGKNE K ELQELKVK ...String:
FASKQSLSYL DGTLPGDYGF DPLGLMDPEG AGGFIDPQWL PYAEIINGRF AMLGAAGAIA PEVLGRIGLI PQETAIPWFQ SGVIPPVGN YSYWADPYTL FVLEMALMGF AEHRRAQDYY KPGSMGKQYF LGLEKFLGGS GNPAYPGGPI FNFLGFGKNE K ELQELKVK EVKNGRLAMM AVLGYFTQAI FTGVGPFQNL LDHLADPVHN NVLTN

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Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Moss (plant)
Molecular weightTheoretical: 22.445592 KDa
SequenceString: GAERPLWLPG TTPPAHLDGT LAGDFGFDPL GLGQDPQDLR WYVQAELVHS RFAMAGVAGI LFTDLLRASG RTDIPVWFEA GATKFDFAD TTTLFVVQLI LMGFVETKRW MDIVKPGSQA AEDSFFGFEA AFEGLETGYP GGPLFNPLGF ANDPTKPQPL R WKEIKNGR ...String:
GAERPLWLPG TTPPAHLDGT LAGDFGFDPL GLGQDPQDLR WYVQAELVHS RFAMAGVAGI LFTDLLRASG RTDIPVWFEA GATKFDFAD TTTLFVVQLI LMGFVETKRW MDIVKPGSQA AEDSFFGFEA AFEGLETGYP GGPLFNPLGF ANDPTKPQPL R WKEIKNGR LAMVAMVGFM VQAYVTKTGP IENLLTHLSD PVHNTII

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Macromolecule #18: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 18 / Number of copies: 144 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #19: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 19 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 20 / 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 #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 26 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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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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Macromolecule #24: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 24 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #25: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 25 / Number of copies: 12 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #26: (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: 26 / 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 #27: (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: 27 / 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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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 70288
FSC plot (resolution estimation)

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