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- EMDB-6929: Cryo-EM structure of the red algal PSI-LHCR -

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Basic information

Entry
Database: EMDB / ID: EMD-6929
TitleCryo-EM structure of the red algal PSI-LHCR
Map data
Sample
  • Complex: PSI-5Lhcr
    • Protein or peptide: x 15 types
  • Ligand: x 11 types
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chloroplast thylakoid membrane / chlorophyll binding ...thylakoid membrane / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chloroplast thylakoid membrane / chlorophyll binding / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / 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 PsaO / PsaO transmembrane domain / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / 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
Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 ...Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote) / Red alga (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsPi X
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga.
Authors: Xiong Pi / Lirong Tian / Huai-En Dai / Xiaochun Qin / Lingpeng Cheng / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic ...Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.
History
DepositionMar 8, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 25, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zgb
  • Surface level: 0.0562
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6929.png

Downloads & links

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Map

FileDownload / File: emd_6929.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å		1.05 Å/pix.
x 280 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0562 / Movie #1: 0.0562
Minimum - Maximum-0.17014694 - 0.6529895
Average (Standard dev.)0.00007548861 (±0.013605257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1700.6530.000

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Supplemental data

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Sample components

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Entire : PSI-5Lhcr

EntireName: PSI-5Lhcr
Components
  • Complex: PSI-5Lhcr
    • Protein or peptide: PsaA
    • Protein or peptide: PsaB
    • Protein or peptide: PsaC
    • Protein or peptide: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: PsaI
    • Protein or peptide: PsaJ
    • Protein or peptide: PsaK
    • Protein or peptide: PsaL
    • Protein or peptide: PsaM
    • Protein or peptide: PsaO
    • Protein or peptide: Lhcr1
    • Protein or peptide: Lhcr2
    • Protein or peptide: Lhcr3
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-D-GLUCOSE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (2S)-2,3-dihydroxypropyl octadecanoate
  • Ligand: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
  • Ligand: 1-DODECANOL

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Supramolecule #1: PSI-5Lhcr

SupramoleculeName: PSI-5Lhcr / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Cyanidioschyzon merolae (eukaryote)

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Macromolecule #1: PsaA

MacromoleculeName: PsaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 82.763461 KDa
SequenceString: MTLTTEKQVK VVVDRDVVPT SFEKWAKPGH FSRSLAKGPK TTTWIWNLHA DAHDFDSHTS SLEEVSRKIF SAHFGQLAII FIWLSGMYF HGARFSNYVA WLSNPTGIKP SAQVVWPIVG QQILNADVGG GMQGIQITSG LFQLWRASGI VNELQLYVTA L GGLGMAGL ...String:
MTLTTEKQVK VVVDRDVVPT SFEKWAKPGH FSRSLAKGPK TTTWIWNLHA DAHDFDSHTS SLEEVSRKIF SAHFGQLAII FIWLSGMYF HGARFSNYVA WLSNPTGIKP SAQVVWPIVG QQILNADVGG GMQGIQITSG LFQLWRASGI VNELQLYVTA L GGLGMAGL MIFAGWFHYH KAAPKLEWFQ NVESMLNHHL AGLLGLGSLS WAGHQIHVSL PINKLLDAGV APSSIPLPHE FI LNRNLMA ELYPSFQQGL VPFFTLNWKQ YSDILTFKGG LSPVTGGLWL TDVAHHHLAI AVLFLVAGHM YRTNWGIGHS IKQ ILEAHK GPLTGEGHKG LYEILTTSWH ANLAINLAML GSLSIIVAHH MYAMPPYPYL ATDYPTQLSL FTHHMWIGGF CIVG AGAHA AIYMVRDYSP TVNFNNVLDR MIRHRDAIIS HLNWVCIFLG MHSFGLYIHN DTMRALGRAQ DMFSDTAIQL QPVFA QWIQ QIHTLAPGNT AVNALATASY AFGADTVTVG SKIAMMPIKL GTADFMVHHI HAFTIHVTTL ILLKGVLYAR NSRLIP DKA NLGFRFPCDG PGRGGTCQVS AWDHVFLGLF WMYNALSIVI FHFSWKMQSD VWGTVTSNGA ISHITGGNFA QSAITIN GW LRDFLWAQAS QVIQSYGSSL SAYGLMFLGA HFVWAFSLMF LFSGRGYWQE LIESIVWAHN KLKVAPAIAP RALSITQG R AVGVAHYLLG GIATTWAFFL ARIIAVG

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Macromolecule #2: PsaB

MacromoleculeName: PsaB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 82.107852 KDa
SequenceString: MATKFPKFSQ ALASDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVAN PLKTKPLAH AIWDPHFGQA ALKAFTRGDT VANISYSGVY HWWYTIGIRN NVELYTGALG LLVLSAVFLL AGWLHIQPKF K PSLSWFKN ...String:
MATKFPKFSQ ALASDPTTRR IWYGIATAHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVAN PLKTKPLAH AIWDPHFGQA ALKAFTRGDT VANISYSGVY HWWYTIGIRN NVELYTGALG LLVLSAVFLL AGWLHIQPKF K PSLSWFKN NESRLNHHLA GLFGVSSLAW TGHLVHVAIP ASRGQHVGWD NFIMTPPHPA GLQPFFTGNW SVYAQSPDSM QH VFGTSQG AGTAILTFLG GFHPQTQSLW LTDMAHHHLA IAVIFIVAGH MYRTNFGIGH NLKTILEAHR PPSGRLGKGH IGI YQTLTN SLHFQLGLAL ASLSVVTSLV AQHMYAMPPY AYMAFDYVTQ SALYTHHQYI AGLLIVGAFA HGAIFFIRDY DPEQ NQDNV LARMLAHKEA VISHLSWVSL FLGFHTLGLY VHNDVVVAFG NPEKQILIEP IFAQWIQATS GKMLYGFQVL LSSST SNAS VAAQQLWLPG WLEAVNNESN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKDFGYS FPCDGP GRG GTCDISAWDA FYLAMFWMLN TIGWVTFYWH WKHLSLWQGN VAQFNESSTY LMGWLRDYLW LNSSPLINGY NPYGMNS LA VWSWMFLFAH LVWATGFMFL ISWRGYWQEL IETLAWAHER TPLANLIRWK DKPVALSIVQ ARLVGLVHFT VGYILTYA A FVIASTAGKF S

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Macromolecule #3: PsaC

MacromoleculeName: PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 8.822272 KDa
SequenceString:
MAHTVKIYDN CIGCTQCVRA CPLDVLEMVP WDGCKAGQMA SAPRTEDCVG CKRCETACPT DFLSIRVYLG GETTRSMGLA Y

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Macromolecule #4: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 15.698932 KDa
SequenceString:
MLNLKMPSPS FLGSTGGWLR CAETEEKYAM TWSSDQQHIF EMPTGGAAVM NSGDNLLYLA RKEQALALAT QLRTQFKIQD YKIYRIFPS GEVQYLHPKD GVLPYQVNKG REQVGRVKST IGKNVNPAQV KFTSKATYDR

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Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 10.545162 KDa
SequenceString:
MIKKGSLVKI LRPESFWYNE VGTVVNVETS KVLYPVLVRF DKVNYSGLNS TNFSLDELVE IKVEIKSDTS AKSPVKPPVK SEVKAEKEN KKEGA

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Macromolecule #6: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 21.239318 KDa
SequenceString:
MFKRSLIFIA AVMSVCQISA IQISAVSADV LTPCQQSEAF HKREINEVRT LENRQANYEA NSPSYLALQS QIDQVHKRFD KYGTLLCGQ DGLPHLITDG DWRHAREFTI PALLFLYITG WIGWVGRSYL KYTKETKNPT EQEIILDVPM ALKYMLSGFL W PLSAWQEY RSGQLLAKED EITVSPR

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Macromolecule #7: PsaI

MacromoleculeName: PsaI / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 3.408184 KDa
SequenceString:
MSASYLPSIL VPTVGLILPF ASMAILFIAI EK

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Macromolecule #8: PsaJ

MacromoleculeName: PsaJ / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 4.410245 KDa
SequenceString:
MNLKKYLSTA PVVATLWLFL TAGILIELNR FFPDSLFY

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Macromolecule #9: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 6.295657 KDa
SequenceString:
MMITIPYTIP TIMVISNLVG VAVGRYALGR SDLTQLIASM CFGHIIGVGI VLGLSNMGVI

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Macromolecule #10: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 15.157522 KDa
SequenceString:
MTDYIKPYNN DPFVGHLATP INSSSLTRAY LSQLPIYRRG VSPFLRGLEI GMAHGYFLIG PFVQLGPLRN TDIKYLAGLL SAIGLIVIL TLGMLLYGAV SFTNDSQDLE SVDGWRQLAS GFLLGAVGGA GFAYLLLTLF S

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Macromolecule #11: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 3.139878 KDa
SequenceString:
MITDNQVFVA LIMALVCGYL AVKLAKQLA

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Macromolecule #12: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 16.744471 KDa
SequenceString:
MYGFVSVLPV ASALQRQQCT CAARCSFTTR AARVAPVRIA LSRPQRLVGA SSLRMFEVSD GEPYPLNPAV IFIALIGWSA VAAIPSNIP VLGGTGLTQA FLASIQRLLA QYPTGPKLDD PFWFYLIVYH VGLFALLIFG QIGYAGYAKG TYNRSA

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Macromolecule #13: Lhcr1

MacromoleculeName: Lhcr1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 19.808818 KDa
SequenceString:
EQSPALPFLS KPPNLSPDMP GYRGFDPLRF SDAFDVNWLQ EGEIKNGRVA MLACLHFFVT EFYQFPFFAG APKLAGPAHD YFVKSGAMI QILAFIGFLE FLLHRGKVLY SDMEWKGRKP GELGFNPLNL PNDKAMRDRE VNNGRLAMLG FAGIIHGEFL N GKMPFEQI TNFQPLQ

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Macromolecule #14: Lhcr2

MacromoleculeName: Lhcr2 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 21.960398 KDa
SequenceString: TRVPARGLRM QAPSGATMPS MPFLKRPSKL DGSLPGGEGC FDPLGFTEVF SLEWLREAEI KHCRVAMLAV LGVIAQEFGT FDFYNAKSK LQLSPDLHNQ FVQNGALQQI LLFVCAWEFI VGLPALIESV NGNREPGYFG FDPLKLGGTV GSAQWKRMQA G ELRNGRLA ...String:
TRVPARGLRM QAPSGATMPS MPFLKRPSKL DGSLPGGEGC FDPLGFTEVF SLEWLREAEI KHCRVAMLAV LGVIAQEFGT FDFYNAKSK LQLSPDLHNQ FVQNGALQQI LLFVCAWEFI VGLPALIESV NGNREPGYFG FDPLKLGGTV GSAQWKRMQA G ELRNGRLA MIAFGGFFHQ QLLTKQGIIE QLAHFNAIKP N

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Macromolecule #15: Lhcr3

MacromoleculeName: Lhcr3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 20.458535 KDa
SequenceString:
TNVARSSGNS RSVPFAPVPE AVRESGLAGS EAEFDPLMIT SYLPISWMRE SEVKHGRIAM LAFVGTLAQQ AYQFPWYKGA PTTLVGAHD HFVTTALAQI LLFTSAFEIV AGVPAAIQTV RGSGRLPGYY GFDPLGLWGK DEASRKRMEL AEVKNGRLAM I AMLALWHQ EVLSGGMGVI EQLVKQKFTP

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Macromolecule #16: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 16 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #17: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 17 / Number of copies: 157 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #18: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 18 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #20: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 20 / Number of copies: 21 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: BETA-D-GLUCOSE

MacromoleculeName: BETA-D-GLUCOSE / type: ligand / ID: 22 / Number of copies: 1 / Formula: BGC
Molecular weightTheoretical: 180.156 Da

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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: (2S)-2,3-dihydroxypropyl octadecanoate

MacromoleculeName: (2S)-2,3-dihydroxypropyl octadecanoate / type: ligand / ID: 24 / Number of copies: 1 / Formula: 3XQ
Molecular weightTheoretical: 358.556 Da
Chemical component information

ChemComp-3XQ:
(2S)-2,3-dihydroxypropyl octadecanoate

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Macromolecule #25: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...

MacromoleculeName: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
type: ligand / ID: 25 / Number of copies: 25 / Formula: ZEX
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-ZEX:
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

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Macromolecule #26: 1-DODECANOL

MacromoleculeName: 1-DODECANOL / type: ligand / ID: 26 / Number of copies: 1 / Formula: 1DO
Molecular weightTheoretical: 186.334 Da
Chemical component information

ChemComp-1DO:
1-DODECANOL

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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

Concentration3.0 mg/mL
BufferpH: 7.4
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.17 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4xk8

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 124279
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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