[English] 日本語
Yorodumi
- EMDB-12228: Red alga C.merolae Photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12228
TitleRed alga C.merolae Photosystem I
Map data
Sample
  • Complex: Photosystem I
    • Protein or peptide: x 15 types
  • Ligand: x 18 types
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / 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 PsaO / 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 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. / 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 reaction center subunit IX / PSI-F / 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 II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 ...Photosystem I reaction center subunit IX / PSI-F / 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 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 strain 10D (eukaryote) / Red alga (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNelson N / Klaiman D / Hippler M
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: To Be Published
Title: Red alga C.merolae Photosystem I
Authors: Nelson N / Klaiman D / Hippler M
History
DepositionJan 19, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7blz
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12228.png

Downloads & links

-
Map

FileDownload / File: emd_12228.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 0.0186 / Movie #1: 0.035
Minimum - Maximum-0.07398664 - 0.16311452
Average (Standard dev.)0.00028240826 (±0.0065125544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z315.600315.600315.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0740.1630.000

-
Supplemental data

-
Half map: #2

Fileemd_12228_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12228_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem I

EntireName: Photosystem I
Components
  • Complex: Photosystem I
    • Protein or peptide: Similar to light harvesting protein
    • Protein or peptide: Similar to chlorophyll a/b-binding protein, CP24
    • Protein or peptide: Lhcr3
    • 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 p700 chlorophyll A apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center subunit VII
    • Protein or peptide: PSI-F
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PSI-K
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: PsaO
  • Ligand: CHLOROPHYLL A
  • Ligand: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: ERGOSTEROL
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: DIACYL GLYCEROLDiglyceride
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: Phosphatidylinositol
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM IONCalcium
  • Ligand: water

+
Supramolecule #1: Photosystem I

SupramoleculeName: Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Cyanidioschyzon merolae strain 10D (eukaryote)

+
Macromolecule #1: Similar to light harvesting protein

MacromoleculeName: Similar to light harvesting protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 19.551574 KDa
SequenceString:
QSPALPFLSK PPNLSPDMPG YRGFDPLRFS DAFDVNWLQE GEIKNGRVAM LACLHFFVTE FYQFPFFAGA PKLAGPAHDY FVKSGAMIQ ILAFIGFLEF LLHRGKVLYS DMEWKGRKPG ELGFNPLNLP NDKAMRDREV NNGRLAMLGF AGIIHGEFLN G KMPFEQIT NFQPL

+
Macromolecule #2: Similar to chlorophyll a/b-binding protein, CP24

MacromoleculeName: Similar to chlorophyll a/b-binding protein, CP24 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 19.79685 KDa
SequenceString:
GATMPSMPFL KRPSKLDGSL PGGEGCFDPL GFTEVFSLEW LREAEIKHCR VAMLAVLGVI AQEFGTFDFY NAKSKLQLSP DLHNQFVQN GALQQILLFV CAWEFIVGLP ALIESVNGNR EPGYFGFDPL KLGGTVGSAQ WKRMQAGELR NGRLAMIAFG G FFHQQLLT KQGIIEQLAH F

+
Macromolecule #3: Lhcr3

MacromoleculeName: Lhcr3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 19.041045 KDa
SequenceString:
VPFAPVPEAV RESGLAGSEA EFDPLMITSY LPISWMRESE VKHGRIAMLA FVGTLAQQAY QFPWYKGAPT TLVGAHDHFV TTALAQILL FTSAFEIVAG VPAAIQTVRG SGRLPGYYGF DPLGLWGKDE ASRKRMELAE VKNGRLAMIA MLALWHQEVL S GGMGVIEQ LVKQKF

+
Macromolecule #4: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 82.215789 KDa
SequenceString: EKQVKVVVDR DVVPTSFEKW AKPGHFSRSL AKGPKTTTWI WNLHADAHDF DSHTSSLEEV SRKIFSAHFG QLAIIFIWLS GMYFHGARF SNYVAWLSNP TGIKPSAQVV WPIVGQQILN ADVGGGMQGI QITSGLFQLW RASGIVNELQ LYVTALGGLG M AGLMIFAG ...String:
EKQVKVVVDR DVVPTSFEKW AKPGHFSRSL AKGPKTTTWI WNLHADAHDF DSHTSSLEEV SRKIFSAHFG QLAIIFIWLS GMYFHGARF SNYVAWLSNP TGIKPSAQVV WPIVGQQILN ADVGGGMQGI QITSGLFQLW RASGIVNELQ LYVTALGGLG M AGLMIFAG WFHYHKAAPK LEWFQNVESM LNHHLAGLLG LGSLSWAGHQ IHVSLPINKL LDAGVAPSSI PLPHEFILNR NL MAELYPS FQQGLVPFFT LNWKQYSDIL TFKGGLSPVT GGLWLTDVAH HHLAIAVLFL VAGHMYRTNW GIGHSIKQIL EAH KGPLTG EGHKGLYEIL TTSWHANLAI NLAMLGSLSI IVAHHMYAMP PYPYLATDYP TQLSLFTHHM WIGGFCIVGA GAHA AIYMV RDYSPTVNFN NVLDRMIRHR DAIISHLNWV CIFLGMHSFG LYIHNDTMRA LGRAQDMFSD TAIQLQPVFA QWIQQ IHTL APGNTAVNAL ATASYAFGAD TVTVGSKIAM MPIKLGTADF MVHHIHAFTI HVTTLILLKG VLYARNSRLI PDKANL GFR FPCDGPGRGG TCQVSAWDHV FLGLFWMYNA LSIVIFHFSW KMQSDVWGTV TSNGAISHIT GGNFAQSAIT INGWLRD FL WAQASQVIQS YGSSLSAYGL MFLGAHFVWA FSLMFLFSGR GYWQELIESI VWAHNKLKVA PAIAPRALSI TQGRAVGV A HYLLGGIATT WAFFLARIIA VG

+
Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 81.976656 KDa
SequenceString: ATKFPKFSQA LASDPTTRRI WYGIATAHDF ESHDGMTEEN LYQKIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEQWVANP LKTKPLAHA IWDPHFGQAA LKAFTRGDTV ANISYSGVYH WWYTIGIRNN VELYTGALGL LVLSAVFLLA GWLHIQPKFK P SLSWFKNN ...String:
ATKFPKFSQA LASDPTTRRI WYGIATAHDF ESHDGMTEEN LYQKIFASHF GHLAIIFLWT SGNLFHVAWQ GNFEQWVANP LKTKPLAHA IWDPHFGQAA LKAFTRGDTV ANISYSGVYH WWYTIGIRNN VELYTGALGL LVLSAVFLLA GWLHIQPKFK P SLSWFKNN ESRLNHHLAG LFGVSSLAWT GHLVHVAIPA SRGQHVGWDN FIMTPPHPAG LQPFFTGNWS VYAQSPDSMQ HV FGTSQGA GTAILTFLGG FHPQTQSLWL TDMAHHHLAI AVIFIVAGHM YRTNFGIGHN LKTILEAHRP PSGRLGKGHI GIY QTLTNS LHFQLGLALA SLSVVTSLVA QHMYAMPPYA YMAFDYVTQS ALYTHHQYIA GLLIVGAFAH GAIFFIRDYD PEQN QDNVL ARMLAHKEAV ISHLSWVSLF LGFHTLGLYV HNDVVVAFGN PEKQILIEPI FAQWIQATSG KMLYGFQVLL SSSTS NASV AAQQLWLPGW LEAVNNESNS LFLTIGPGDF LVHHAIALGL HTTTLILVKG ALDARGSKLM PDKKDFGYSF PCDGPG RGG TCDISAWDAF YLAMFWMLNT IGWVTFYWHW KHLSLWQGNV AQFNESSTYL MGWLRDYLWL NSSPLINGYN PYGMNSL AV WSWMFLFAHL VWATGFMFLI SWRGYWQELI ETLAWAHERT PLANLIRWKD KPVALSIVQA RLVGLVHFTV GYILTYAA F VIASTAGKFS

+
Macromolecule #6: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 8.691076 KDa
SequenceString:
AHTVKIYDNC IGCTQCVRAC PLDVLEMVPW DGCKAGQMAS APRTEDCVGC KRCETACPTD FLSIRVYLGG ETTRSMGLAY

+
Macromolecule #7: Photosystem I p700 chlorophyll A apoprotein A2

MacromoleculeName: Photosystem I p700 chlorophyll A apoprotein A2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 15.567736 KDa
SequenceString:
LNLKMPSPSF LGSTGGWLRC AETEEKYAMT WSSDQQHIFE MPTGGAAVMN SGDNLLYLAR KEQALALATQ LRTQFKIQDY KIYRIFPSG EVQYLHPKDG VLPYQVNKGR EQVGRVKSTI GKNVNPAQVK FTSKATYDR

+
Macromolecule #8: Photosystem I iron-sulfur center subunit VII

MacromoleculeName: Photosystem I iron-sulfur center subunit VII / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 6.98504 KDa
SequenceString:
IKKGSLVKIL RPESFWYNEV GTVVNVETSK VLYPVLVRFD KVNYSGLNST NFSLDELVEI K

+
Macromolecule #9: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 17.997396 KDa
SequenceString:
VLTPCQQSEA FHKREINEVR TLENRQANYE ANSPSYLALQ SQIDQVHKRF DKYGTLLCGQ DGLPHLITDG DWRHAREFTI PALLFLYIT GWIGWVGRSY LKYTKETKNP TEQEIILDVP MALKYMLSGF LWPLSAWQEY RSGQLLAKED EITVSP

+
Macromolecule #10: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 3.276988 KDa
SequenceString:
SASYLPSILV PTVGLILPFA SMAILFIAIE K

+
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: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 4.410245 KDa
SequenceString:
MNLKKYLSTA PVVATLWLFL TAGILIELNR FFPDSLFY

+
Macromolecule #12: PSI-K

MacromoleculeName: PSI-K / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 5.608732 KDa
SequenceString:
YTIPTIMVIS NLVGVAVGRY ALGRSDLTQL IASMCFGHII GVGIVLGLSN MGVI

+
Macromolecule #13: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 14.69097 KDa
SequenceString:
DYIKPYNNDP FVGHLATPIN SSSLTRAYLS QLPIYRRGVS PFLRGLEIGM AHGYFLIGPF VQLGPLRNTD IKYLAGLLSA IGLIVILTL GMLLYGAVSF TNDSQDLESV DGWRQLASGF LLGAVGGAGF AYLLLTL

+
Macromolecule #14: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 2.937604 KDa
SequenceString:
ITDNQVFVAL IMALVCGYLA VKLAKQL

+
Macromolecule #15: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Red alga (eukaryote) / Strain: 10D
Molecular weightTheoretical: 10.485055 KDa
SequenceString:
FEVSDGEPYP LNPAVIFIAL IGWSAVAAIP SNIPVLGGTG LTQAFLASIQ RLLAQYPTGP KLDDPFWFYL IVYHVGLFAL LIFGQIGYA GYAKGTYN

+
Macromolecule #16: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 16 / Number of copies: 132 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #17: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca- ...Name: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 17 / Number of copies: 13 / Formula: C7Z
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-C7Z:
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol

+
Macromolecule #18: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 18 / Number of copies: 5 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol / Β-Cryptoxanthin

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 6 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #20: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 20 / Number of copies: 3 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL / Ergosterol

+
Macromolecule #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 22 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #22: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 22 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #23: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 23 / Number of copies: 2 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

+
Macromolecule #24: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 2 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #25: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 25 / Number of copies: 4 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #26: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 26 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

+
Macromolecule #27: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 27 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #28: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 28 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 29 / Number of copies: 3 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

+
Macromolecule #30: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 30 / Number of copies: 1 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

+
Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #32: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 249 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

-
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 K3 BIOQUANTUM (6k x 4k) / Number real images: 7220 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1198564
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5zgh

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 8 / Avg.num./class: 16117 / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
Final reconstructionNumber classes used: 8 / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 128943
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7blz:
Red alga C.merolae Photosystem I

+
About Yorodumi

-
News

-
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

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • 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

-
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

Read more