[English] 日本語
Yorodumi
- EMDB-37480: PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37480
TitlePSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Map data
Sample
  • Complex: PSI-LHCI
    • Protein or peptide: x 15 types
  • Ligand: x 11 types
KeywordsPhotosystem I / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Biological speciesCyanidium caldarium (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsKato K / Hamaguchi T / Nakajima Y / Kawakami K / Yonekura K / Shen JR / Nagao R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: The structure of PSI-LHCI from provides evolutionary insights into conservation and diversity of red-lineage LHCs.
Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / ...Authors: Koji Kato / Tasuku Hamaguchi / Minoru Kumazawa / Yoshiki Nakajima / Kentaro Ifuku / Shunsuke Hirooka / Yuu Hirose / Shin-Ya Miyagishima / Takehiro Suzuki / Keisuke Kawakami / Naoshi Dohmae / Koji Yonekura / Jian-Ren Shen / Ryo Nagao /
Abstract: Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the ...Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between and , whereas no orthologous relationships were found between Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
History
DepositionSep 19, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37480.png

Downloads & links

-
Map

FileDownload / File: emd_37480.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 256 pix.
= 202.752 Å		0.79 Å/pix.
x 256 pix.
= 202.752 Å		0.79 Å/pix.
x 256 pix.
= 202.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.792 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.106468886 - 0.28850564
Average (Standard dev.)0.00058164407 (±0.0068250606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 202.752 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_37480_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37480_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37480_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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: 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 X
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I subunit O
    • 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: DODECYL-BETA-D-MALTOSIDE
  • Ligand: UNKNOWN LIGAND
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: Zeaxanthin
  • Ligand: water

+
Supramolecule #1: PSI-LHCI

SupramoleculeName: PSI-LHCI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 550 KDa

+
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
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 82.698344 KDa
SequenceString: MTLTTDKKVK VVVDRDVVAT SFEKWAKPGH FSRSLAKGPK TTTWIWNLHA DAHDFDSHTS SLEEVSRKIF SAHFGQLAII FIWLSGMYF HGARFSNYVA WLSNPTGIKP SAQVVWPIVG QQILNADVGG GIQGIQITSG LFQLWRASGI VNELQLYVTA I GGLVMAGL ...String:
MTLTTDKKVK VVVDRDVVAT SFEKWAKPGH FSRSLAKGPK TTTWIWNLHA DAHDFDSHTS SLEEVSRKIF SAHFGQLAII FIWLSGMYF HGARFSNYVA WLSNPTGIKP SAQVVWPIVG QQILNADVGG GIQGIQITSG LFQLWRASGI VNELQLYVTA I GGLVMAGL MMFAGWFHYH KAAPKLEWFQ NVESMLNHHL AGLLGLGSLS WAGHQIHVSL PVNKLLDAGV APSSIPLPHE FI LNRNLMA ELYPSFQQGL APFFTLNWKQ YSDILTFKGG LSPVTGGLWL TDVAHHHLAI AVLFIVAGHM YRTNWGIGHS MKQ LLEAHK GPLTGEGHKG LYEVLTTSWH ANLAINLAML GSLSIIVAHH MYSMPPYPYL ATDYPTQLSL FTHHMWIGGF CIVG AGAHA AIYMVRDYSP TVNYNNVLDR MIRHRDAIIS HLNWVCIFLG THSFGLYIHN DTMRALGRAQ DMFSDTAIQL QPVLA QWIQ QIHTLAPGNT AVNALATASY AFGADTVTVG SKIAMMPIKL GTADFMVHHI HAFTIHVTVL ILLKGVLFAR NSRLIP DKA NLGFRFPCDG PGRGGTCQVS AWDHVFLGLF WMYNALSVVI FHFSWKMQSD VWGTVSSNGT VSHITGGNFA QSAITIN GW LRDFLWAQAS QVIQSYGSSL SAYGLMFLGA HFVWAFSLMF LFSGRGYWQE LIESIVWAHN KLKVAPSIAP RALSITQG R AVGVAHYLLG GIATTWAFFL ARIISVG

+
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
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 82.160898 KDa
SequenceString: MTTKFPKFSQ ALASDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHLALIFLW TSGNLFHVAW QGNFEQWIAN PLKTKPLAH AIWDPHFGQA ALKAFTRGET VANISYSGLY HWWYTIGLRN NVELYSGALG LLVLSAVFLL AGWLHIQPKF K PSLSWFKN ...String:
MTTKFPKFSQ ALASDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHLALIFLW TSGNLFHVAW QGNFEQWIAN PLKTKPLAH AIWDPHFGQA ALKAFTRGET VANISYSGLY HWWYTIGLRN NVELYSGALG LLVLSAVFLL AGWLHIQPKF K PSLSWFKN NESRLNHHLA GLFGVSSLAW TGHLVHVAIP ASRGQHVGWD NFISVAPHPA GLQPFFTGNW SVYAQSPDSM QH VFGTNQG AGTAILTFLG GFHPQTQSLW LTDMAHHHLA IAVIFIVAGH MYRTNFGIGH NLKTILEAHR PPSGRLGKGH IGI YQTLTN SLHFQLGLAL ACLSVVTSLV AQHMYAMPPY AYMAYDYVTQ AALYTHHQYI AGLLIVGAFA HGAIFFIRDY DPEQ NQDNV LARMLTHKEA IISHLSWVSL FLGFHTLGLY VHNDVVVAFG NPEKQILIEP IFAQWIQATS GKALYGFHVL LSSST SNAT TAAQQLWLPG WLEAINNESN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKDFGYS FPCDGP GRG GTCDISAWDA FYLAMFWMLN TIGWITFYWH WKHLSLWQGN VAQFNESSTY LMGWLRDYLW LNSSPLINGY NPYGMNS LS VWAWMFLFAH LVWATGFMFL ISWRGYWQEL IETLAWAHER TPLANLIKWK DKPVALSIVQ ARLVGLVHFT VGYILTYA A FVIASTAGKF S

+
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
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 8.822272 KDa
SequenceString:
MAHTVKIYDN CIGCTQCVRA CPLDVLEMVP WDGCKAGQMA SAPRTEDCVG CKRCETACPT DFLSIRVYLG GETTRSMGLA Y

+
Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 15.709957 KDa
SequenceString:
MLNLKMPSPN FLGSTGGWLR CAETEEKYAM TWSSNREHVF EMPTGGAATM NAGDNLLYLA RKEQALALAT QLRTQFKIQD YKIYRIFPS GEVQYLHPKD GVLPYLVNEG REQVGRIKAT IGKNVNPAQV KFTSKATYDR

+
Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 6.974055 KDa
SequenceString:
MLKKGSLVKI LRPESYWFNE VGTVVSVETS KVLYPVLVRF EKVNYSGLNS TSFALEELQE I

+
Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 20.520506 KDa
SequenceString:
MKLSRLFILA CMCVCVDGAT ADVLTTCQQN EAFHKREANE IRQLQNRQSK YDANSGGYLA LQAQIDQVHK RFDKYGELLC GQDGLPHLI TDGDWRHARE FTIPAILFLY ITGWIGWVGR SYLQYTKQTK NPTEQEIILD LPMAFKYMLS GFLWPLSAWQ E YRSGKLLA KEDEISVSPR

+
Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 3.408183 KDa
SequenceString:
MSASYLPSIL VPTVGLILPF ATMAILFVAI EK

+
Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 4.426245 KDa
SequenceString:
MNLKKYLSTA PVVATLWLFL TAGILIELNR FYPDSLFY

+
Macromolecule #9: Photosystem I reaction center subunit X

MacromoleculeName: Photosystem I reaction center subunit X / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 7.105433 KDa
SequenceString:
MIQFPSSIPV IMVISNLLAL AIGRYAIQNP SNETPIIGLN LAQLVATTSF GHIIGVATIL GLSNMGII

+
Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 15.343729 KDa
SequenceString:
MSDYIKPYNN DPFVGHLATP INSSSLTRGY LAQLPIYRSG LSPFLRGLEI GMAHGYFLIG PFVELGPLRN TEMKYLAGLL SAVGLVVIL TLGMLLYGYV SFTNDSQDVE SLEGWRQLAS GFLLGAVGGA GFAYLLIYSF IL

+
Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 3.010698 KDa
SequenceString:
MITDNQVFVA LIMALVCGYL AVKLAAQL

+
Macromolecule #12: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 16.661221 KDa
SequenceString:
MYGFVSVLPV ASGVQRGQFA CTSLKGFHGR VARFQQARLP SAGRARSVGA SSLRMFEISD GEQYPLNPAV ILIAIIGWSA AAAVPSNIP VLGGTGLTQA FLASIQRLLA QYPTGPKLDD PFWFYLVVYH VGLFALLIFG QIGYAGYARG TYKRSS

+
Macromolecule #13: Lhcr1

MacromoleculeName: Lhcr1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 24.117104 KDa
SequenceString: MYAFVSAVPL AQRSKLCLKK TNGRSLNRDC AFGYGTLRME QSPAMPFLSK PPNLSPDMPG YRGFDPLRLS DAFDVNWLLE GEVKNGRVA MLACLHFFVT EYYQFPFYAG APKLAAPAHD YFVKSGAMIQ ILVFIGFLEM VLHRGKVLYS DMEWKGRKPG E LGFNPLNL ...String:
MYAFVSAVPL AQRSKLCLKK TNGRSLNRDC AFGYGTLRME QSPAMPFLSK PPNLSPDMPG YRGFDPLRLS DAFDVNWLLE GEVKNGRVA MLACLHFFVT EYYQFPFYAG APKLAAPAHD YFVKSGAMIQ ILVFIGFLEM VLHRGKVLYS DMEWKGRKPG E LGFNPLNL PNDKAMKDRE INNGRLAMLG FAGIIHGEFL NGKMPIEQIT NFQPLQ

+
Macromolecule #14: Lhcr2

MacromoleculeName: Lhcr2 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 24.128066 KDa
SequenceString: MAFISALSCA SLKTGVVGRK VCGLKGAAAG LRMQAPSGAA MPSMPFLKRP SKLDGSLPGG EGCFDPLGFT EVFSLEWMRE AEVKHCRVA MLAVLGVIAQ EFGTLDFYHA QSKLQLSPDL HNQFVQNGAL QQVLLFVCAW EFFVGLPALI ESLEGRREPG Y FGFDPLKL ...String:
MAFISALSCA SLKTGVVGRK VCGLKGAAAG LRMQAPSGAA MPSMPFLKRP SKLDGSLPGG EGCFDPLGFT EVFSLEWMRE AEVKHCRVA MLAVLGVIAQ EFGTLDFYHA QSKLQLSPDL HNQFVQNGAL QQVLLFVCAW EFFVGLPALI ESLEGRREPG Y FGFDPLKL GGTYGSAQWK RMAAGELRNG RLAMIAFGGF FHQQLLTKQG IIEQLTHFSP LKSS

+
Macromolecule #15: Lhcr3

MacromoleculeName: Lhcr3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanidium caldarium (eukaryote)
Molecular weightTheoretical: 23.826514 KDa
SequenceString: MFVWTSTWVA GGVLGSVSQR RGVCVSRQLR MTEAARDSGT SRSVPFVPAP AAVRKSGLAG SEAEFDPLQI TSYLPISWMR ESEVKHGRI AMLAFVGTLA QQAYQFPWYK GAPTTLVGAH DHFVTTALAQ ILLFTSAFEI LAGVPAAIQT VRGSGRLPGY Y GFDPLGLW ...String:
MFVWTSTWVA GGVLGSVSQR RGVCVSRQLR MTEAARDSGT SRSVPFVPAP AAVRKSGLAG SEAEFDPLQI TSYLPISWMR ESEVKHGRI AMLAFVGTLA QQAYQFPWYK GAPTTLVGAH DHFVTTALAQ ILLFTSAFEI LAGVPAAIQT VRGSGRLPGY Y GFDPLGLW GKDEASRKRM ELAEVKNGRL AMIAMLALWH QEALSGGMGV IEQLVKQKFT P

+
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

+
Macromolecule #17: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 17 / Number of copies: 153 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
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

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #20: BETA-CAROTENE

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

ChemComp-BCR:
BETA-CAROTENE

+
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

+
Macromolecule #22: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 22 / Number of copies: 7 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

+
Macromolecule #23: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 23 / Number of copies: 25 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

+
Macromolecule #24: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 24 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #25: Zeaxanthin

MacromoleculeName: Zeaxanthin / type: ligand / ID: 25 / Number of copies: 23 / Formula: 5X6
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-K3I:
Zeaxanthin

+
Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 560 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.83 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMMES-NaOHMES
0.03 %DDMDDM
GridModel: Quantifoil R0.6/1 / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 39.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

+
Image processing

Startup modelType of model: INSILICO MODEL
In silico model: An initial model was generated de novo from 2D classification.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 228449
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: homology model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8wey:
PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)

+
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