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- EMDB-9807: Structure of PSI tetramer from Anabaena -

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Basic information

Entry
Database: EMDB / ID: EMD-9807
TitleStructure of PSI tetramer from Anabaena
Map data
Sample
  • Complex: PSI tetramer
    • Protein or peptide: x 12 types
  • Ligand: x 7 types
KeywordsPhotosystem / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / 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 / 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
Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI ...Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKato K / Nagao R
CitationJournal: Nat Commun / Year: 2019
Title: Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.
Authors: Koji Kato / Ryo Nagao / Tian-Yi Jiang / Yoshifumi Ueno / Makio Yokono / Siu Kit Chan / Mai Watanabe / Masahiko Ikeuchi / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a ...Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.
History
DepositionFeb 6, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
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  • Surface view colored by height
  • Surface level: 0.06
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  • Surface view with fitted model
  • Atomic models: PDB-6jeo
  • Surface level: 0.06
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9807.png

Downloads & links

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Map

FileDownload / File: emd_9807.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 440 pix.
= 492.8 Å		1.12 Å/pix.
x 440 pix.
= 492.8 Å		1.12 Å/pix.
x 440 pix.
= 492.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.12942305 - 0.26028016
Average (Standard dev.)0.00065376825 (±0.006231211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 492.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z492.800492.800492.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.1290.2600.001

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Supplemental data

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Sample components

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Entire : PSI tetramer

EntireName: PSI tetramer
Components
  • Complex: PSI tetramer
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 1
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK 1
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I 4.8 kDa protein
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: PSI tetramer

SupramoleculeName: PSI tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Molecular weightTheoretical: 1.44 MDa

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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: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 83.28968 KDa
SequenceString: MTISPPEREE KKARVIVDKD PVPTSFEKWA QPGHFDRTLA RGPKTTTWIW NLHALAHDFD THTSDLEDIS RKIFAAHFGH LAVVTIWLS GMIFHGAKFS NYEAWLSDPL NVRPSAQVVW PIVGQDILNG DVGGGFHGIQ ITSGLFQVWR GWGITNSFQL Y CTAIGGLV ...String:
MTISPPEREE KKARVIVDKD PVPTSFEKWA QPGHFDRTLA RGPKTTTWIW NLHALAHDFD THTSDLEDIS RKIFAAHFGH LAVVTIWLS GMIFHGAKFS NYEAWLSDPL NVRPSAQVVW PIVGQDILNG DVGGGFHGIQ ITSGLFQVWR GWGITNSFQL Y CTAIGGLV LAGLFLFAGW FHYHKRAPKL EWFQNVESML NHHLQVLLGC GSLGWAGHLI HVSAPINKLM DAGVAVKDIP LP HEFILNK SLLIDLFPGF AAGLTPFFTL NWGQYADFLT FKGGLNPVTG GLWMTDIAHH HLAIAVVFII AGHQYRTNWG IGH SIKEIL ENHKGPFTGE GHKGLYENLT TSWHAQLATN LAFLGSLTII IAHHMYAMPP YPYLATDYAT QLCIFTHHIW IGGF LIVGG AAHAAIFMVR DYDPVVNQNN VLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMRAL GRPQDMFSDT AIQLQ PVFA QWVQNLHTLA PGGTAPNALE PVSYAFGGGV LAVGGKVAMM PIALGTADFL IHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSGWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVD AAGNVSHITG GNFAQSA IT INGWLRDFLW AQASQVINSY GSALSAYGLM FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALS I TQGRAVGVAH YLLGGIATTW AFFHAHILSV G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2 1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 83.457016 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYAMAMGND FESHDGMTEE NLYQKIFATH FGHLAIIFLW ASSLLFHVAW QGNFEQWIKD PLHVRPIAH AIWDPHFGKP AIEAFTQAGA NGPVNIAYSG VYHWWYTIGM RTNTELYTGS VFLLLFASLF LFAGWLHLQP K FRPSLAWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYAMAMGND FESHDGMTEE NLYQKIFATH FGHLAIIFLW ASSLLFHVAW QGNFEQWIKD PLHVRPIAH AIWDPHFGKP AIEAFTQAGA NGPVNIAYSG VYHWWYTIGM RTNTELYTGS VFLLLFASLF LFAGWLHLQP K FRPSLAWF KSAESRLNHH LAGLFGVSSL AWAGHLIHVA IPESRGQHVG WDNFLSTAPH PAGLQPFFTG NWGVYAQNPD TA GHIFSTS QGAGTAILTF LGGFHPQTES LWLTDMAHHH LAIAVLFIVA GHMYRTNFGI GHSIKEMMNA KTFFGKPVEG PFN MPHQGI YDTYNNSLHF QLGWHLACLG VVTSWVAQHM YSLPSYAFIA KDYTTQAALY THHQYIAIFL MVGAFAHGAI FLVR DYDPE QNKGNVLERV LQHKEAIISH LSWVSLFLGF HTLGLYVHND VVVAFGTPEK QILIEPVFAQ FIQAAHGKVL YGLDT LLSN PDSVAYTAYP NYANVWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTTLILVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDSF YLSLFWALNT VGWVTFYWHW KHLGIWQGNV AQFNENSTYL MGWFRDYLWA NSAQLIN GY NPYGVNNLSV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETLVWAHERT PIANLVRWKD KPVALSIVQA RVVGLAHF T VGYVLTYAAF LIASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2 1

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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: 4 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 8.825206 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAAQVA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 15.17624 KDa
SequenceString:
MAETLSGKTP LFAGSTGGLL TKAVEEEKYA ITWTSPKAQV FELPTGGAAT MHEGENLLYI ARKEYGIALG GQLRKFKITN YKIYRILPS GETTFIHPAD GVFPEKVNAG REKVRFNARS IGENPNPSQV KFSGKATYDA

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 7.897051 KDa
SequenceString:
MVQRGSKVRI LRPESYWFQD VGTVASVDQS GIKYPVIVRF DKVNYAGINT NNFAVDELIE VEAPKAKAKK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 17.850568 KDa
SequenceString:
MRRLFALILV ICLSFSFAPP AKALGADLTP CAENPAFQAL AKNARNTTAD PQSGQKRFER YSQALCGPEG YPHLIVDGRL DRAGDFLIP SILFLYIAGW IGWVGRAYLQ AIKKDSDTEQ KEIQLDLGIA LPIIATGFAW PAAAVKELLS GELTAKDSEI T VSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 5.066925 KDa
SequenceString:
MATAFLPSIL ADASFLSSIF VPVIGWVVPI ATFSFLFLYI EREDVA

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 5.499422 KDa
SequenceString:
MADKADQSSY LIKFISTAPV AATIWLTITA GILIEFNRFF PDLLFHPLP

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 8.852457 KDa
SequenceString:
MLTSTLLAAA TTPLEWSPTV GIIMVIANVI AITFGRQTIK YPSAEPALPS AKFFGGFGAP ALLATTAFGH ILGVGLVLGL HNLGRI

UniProtKB: Photosystem I reaction center subunit PsaK 1

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 18.130725 KDa
SequenceString:
MAQAVDASKN LPSDPRNREV VFPAGRDPQW GNLETPVNAS PLVKWFINNL PAYRPGLTPF RRGLEVGMAH GYFLFGPFAK LGPLRDAAN ANLAGLLGAI GLVVLFTLAL SLYANSNPPT ALASVTVPNP PDAFQSKEGW NNFASAFLIG GIGGAVVAYF L TSNLALIQ GLVG

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 4.42425 KDa
SequenceString:
MPTLYLAQVS SISDTQVYIA LVVALIPGLL AWRLATELYK

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Photosystem I 4.8 kDa protein

MacromoleculeName: Photosystem I 4.8 kDa protein / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 4.872792 KDa
SequenceString:
MAKAKISPVA NTGAKPPYTF RTGWALLLLA VNFLVAAYYF HIIQ

UniProtKB: Photosystem I 4.8 kDa protein

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Macromolecule #13: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 13 / Number of copies: 4 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 376 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #15: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 15 / Number of copies: 8 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #16: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 16 / Number of copies: 12 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #17: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 17 / Number of copies: 88 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 18 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #19: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 19 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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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

Concentration0.014 mg/mL
BufferpH: 6.5 / Component:
ConcentrationFormula
20.0 mMMES-NaOH
0.04 %DDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
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: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 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

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The initial model for the first 3D classification was generated de novo from 2D classification.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 111400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1jb0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6jeo:
Structure of PSI tetramer from Anabaena

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

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

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Yorodumi

Thousand views of thousand structures

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

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

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