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- EMDB-66073: PSI complex of A.thaliana isolated using DOC based Clear-Native-P... -

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Basic information

Entry
Database: EMDB / ID: EMD-66073
TitlePSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
Map data
Sample
  • Complex: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
    • Protein or peptide: x 17 types
  • Ligand: x 13 types
KeywordsPhotosystem I complex / membrane protein / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / calmodulin binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein / 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 reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / 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 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
Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic ...Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsKawamoto A / Seki S / Kurisu G
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
Japan Society for the Promotion of Science (JSPS)23H04960 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 2, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66073.png

Downloads & links

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Map

FileDownload / File: emd_66073.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 392 pix.
= 264.6 Å		0.68 Å/pix.
x 392 pix.
= 264.6 Å		0.68 Å/pix.
x 392 pix.
= 264.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00994
Minimum - Maximum-0.03905465 - 0.10092798
Average (Standard dev.)0.00024124693 (±0.0023128507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 264.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66073_msk_1.map
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Additional map: #1

Fileemd_66073_additional_1.map
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Half map: #2

Fileemd_66073_half_map_1.map
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Half map: #1

Fileemd_66073_half_map_2.map
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Sample components

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Entire : PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method

EntireName: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
Components
  • Complex: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
    • Protein or peptide: Chlorophyll a-b binding protein 6, chloroplastic
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
    • Protein or peptide: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 4, chloroplastic
    • 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-2, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV A, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VI-2, chloroplastic
    • 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, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit XI, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit N, chloroplastic
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: UNKNOWN LIGAND
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: Lutein
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: water

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Supramolecule #1: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method

SupramoleculeName: PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Chlorophyll a-b binding protein 6, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 6, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.021895 KDa
SequenceString: MASNSLMSCG IAAVYPSLLS SSKSKFVSAG VPLPNAGNVG RIRMAAHWMP GEPRPAYLDG SAPGDFGFDP LGLGEVPANL ERYKESELI HCRWAMLAVP GILVPEALGY GNWVKAQEWA ALPGGQATYL GNPVPWGTLP TILAIEFLAI AFVEHQRSME K DPEKKKYP ...String:
MASNSLMSCG IAAVYPSLLS SSKSKFVSAG VPLPNAGNVG RIRMAAHWMP GEPRPAYLDG SAPGDFGFDP LGLGEVPANL ERYKESELI HCRWAMLAVP GILVPEALGY GNWVKAQEWA ALPGGQATYL GNPVPWGTLP TILAIEFLAI AFVEHQRSME K DPEKKKYP GGAFDPLGYS KDPKKLEELK VKEIKNGRLA LLAFVGFCVQ QSAYPGTGPL ENLATHLADP WHNNIGDIVI PF N

UniProtKB: Chlorophyll a-b binding protein 6, chloroplastic

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Macromolecule #2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.782814 KDa
SequenceString: MASSLCASSA IAAISSPSFL GGKKLRLKKK LTVPAVSRPD ASVRAVAADP DRPIWFPGST PPEWLDGSLP GDFGFDPLGL SSDPDSLKW NVQAEIVHCR WAMLGAAGIF IPEFLTKIGI LNTPSWYTAG EQEYFTDKTT LFVVELILIG WAEGRRWADI I KPGSVNTD ...String:
MASSLCASSA IAAISSPSFL GGKKLRLKKK LTVPAVSRPD ASVRAVAADP DRPIWFPGST PPEWLDGSLP GDFGFDPLGL SSDPDSLKW NVQAEIVHCR WAMLGAAGIF IPEFLTKIGI LNTPSWYTAG EQEYFTDKTT LFVVELILIG WAEGRRWADI I KPGSVNTD PVFPNNKLTG TDVGYPGGLW FDPLGWGSGS PAKLKELRTK EIKNGRLAML AVMGAWFQHI YTGTGPIDNL FA HLADPGH ATIFAAFTPK

UniProtKB: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic

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Macromolecule #3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic

MacromoleculeName: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 29.206311 KDa
SequenceString: MAAQALVSSS LTSSVQTARQ IFGSKPVASA SQKKSSFVVK AAATPPVKQG ANRPLWFASS QSLSYLDGSL PGDYGFDPLG LSDPEGTGG FIEPRWLAYG EIINGRFAML GAAGAIAPEI LGKAGLIPAE TALPWFQTGV IPPAGTYTYW ADNYTLFVLE M ALMGFAEH ...String:
MAAQALVSSS LTSSVQTARQ IFGSKPVASA SQKKSSFVVK AAATPPVKQG ANRPLWFASS QSLSYLDGSL PGDYGFDPLG LSDPEGTGG FIEPRWLAYG EIINGRFAML GAAGAIAPEI LGKAGLIPAE TALPWFQTGV IPPAGTYTYW ADNYTLFVLE M ALMGFAEH RRLQDWYNPG SMGKQYFLGL EKGLAGSGNP AYPGGPFFNP LGFGKDEKSL KELKLKEVKN GRLAMLAILG YF IQGLVTG VGPYQNLLDH LADPVNNNVL TSLKFH

UniProtKB: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic

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Macromolecule #4: Chlorophyll a-b binding protein 4, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 4, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.760461 KDa
SequenceString: MATVTTHASA SIFRPCTSKP RFLTGSSGRL NRDLSFTSIG SSAKTSSFKV EAKKGEWLPG LASPDYLTGS LAGDNGFDPL GLAEDPENL KWFVQAELVN GRWAMLGVAG MLLPEVFTKI GIINVPEWYD AGKEQYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN ...String:
MATVTTHASA SIFRPCTSKP RFLTGSSGRL NRDLSFTSIG SSAKTSSFKV EAKKGEWLPG LASPDYLTGS LAGDNGFDPL GLAEDPENL KWFVQAELVN GRWAMLGVAG MLLPEVFTKI GIINVPEWYD AGKEQYFASS STLFVIEFIL FHYVEIRRWQ D IKNPGSVN QDPIFKQYSL PKGEVGYPGG IFNPLNFAPT QEAKEKELAN GRLAMLAFLG FVVQHNVTGK GPFENLLQHL SD PWHNTIV QTFN

UniProtKB: Chlorophyll a-b binding protein 4, chloroplastic

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Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 83.315367 KDa
SequenceString: MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALVFAA ...String:
MIIRSPEPEV KILVDRDPIK TSFEEWAKPG HFSRTIAKGP DTTTWIWNLH ADAHDFDSHT SDLEEISRKV FSAHFGQLSI IFLWLSGMY FHGARFSNYE AWLSDPTHIG PSAQVVWPIV GQEILNGDVG GGFRGIQITS GFFQIWRASG ITSELQLYCT A IGALVFAA LMLFAGWFHY HKAAPKLAWF QDVESMLNHH LAGLLGLGSL SWAGHQVHVS LPINQFLNAG VDPKEIPLPH EF ILNRDLL AQLYPSFAEG ATPFFTLNWS KYSEFLTFRG GLDPVTGGLW LTDIAHHHLA IAILFLIAGH MYRTNWGIGH GIK DILEAH KGPFTGQGHK GLYEILTTSW HAQLSLNLAM LGSLTIIVAH HMYSMPPYPY LATDYATQLS LFTHHMWIGG FLIV GAAAH AAIFMVRDYD PTNRYNDLLD RVLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMSALGRP QDMFSDTAIQ LQPVF AQWI QNTHALAPGV TAPGETASTS LTWGGGELVA VGGKVALLPI PLGTADFLVH HIHAFTIHVT VLILLKGVLF ARSSRL IPD KANLGFRFPC DGPGRGGTCQ VSAWDHVFLG LFWMYNAISV VIFHFSWKMQ SDVWGSISDQ GVVTHITGGN FAQSSIT IN GWLRDFLWAQ ASQVIQSYGS SLSAYGLFFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAT QPRALSII Q GRAVGVTHYL LGGIATTWAF FLARIIAVG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 82.555883 KDa
SequenceString: MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFETWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSALS LIGGWLHLQP K WKPRVSWF ...String:
MALRFPRFSQ GLAQDPTTRR IWFGIATAHD FESHDDITEE RLYQNIFASH FGQLAIIFLW TSGNLFHVAW QGNFETWVQD PLHVRPIAH AIWDPHFGQP AVEAFTRGGA LGPVNIAYSG VYQWWYTIGL RTNEDLYTGA LFLLFLSALS LIGGWLHLQP K WKPRVSWF KNAESRLNHH LSGLFGVSSL AWTGHLVHVA IPASRGEYVR WNNFLNVLPH PQGLGPLFTG QWNLYAQNPD SS SHLFGTS QGSGTAILTL LGGFHPQTQS LWLTDMAHHH LAIAILFLIA GHMYRTNFGI GHSIKDLLEA HIPPGGRLGR GHK GLYDTI NNSIHFQLGL ALASLGVITS LVAQHMYSLP AYAFIAQDFT TQAALYTHHQ YIAGFIMTGA FAHGAIFFIR DYNP EQNED NVLARMLDHK EAIISHLSWA SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPIFAQWIQS AHGKTSYGFD VLLSS TSGP AFNAGRSIWL PGWLNAINEN SNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAVFWM LNTIGWVTFY WHWKHITLWQ GNVSQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLIR WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #7: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.049509 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPTDVLEMIP WDGCKAKQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLW HETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #8: Photosystem I reaction center subunit II-2, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II-2, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.336598 KDa
SequenceString: MATQAAGIFS PAITTTTSAV KKLHLFSSSH RPKSLSFTKT AIRAEKTESS SAAPAVKEAP VGFTPPQLDP NTPSPIFAGS TGGLLRKAQ VEEFYVITWN SPKEQIFEMP TGGAAIMREG PNLLKLARKE QCLALGTRLR SKYKITYQFY RVFPNGEVQY L HPKDGVYP ...String:
MATQAAGIFS PAITTTTSAV KKLHLFSSSH RPKSLSFTKT AIRAEKTESS SAAPAVKEAP VGFTPPQLDP NTPSPIFAGS TGGLLRKAQ VEEFYVITWN SPKEQIFEMP TGGAAIMREG PNLLKLARKE QCLALGTRLR SKYKITYQFY RVFPNGEVQY L HPKDGVYP EKANPGREGV GLNMRSIGKN VSPIEVKFTG KQSYDL

UniProtKB: Photosystem I reaction center subunit II-2, chloroplastic

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Macromolecule #9: Photosystem I reaction center subunit IV A, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV A, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.984955 KDa
SequenceString:
MAMTTASTVF VLPANVTSVA GASSSRSSVS FLPMRNAGSR LVVRAAEDPA PASSSSKDSP AAAAAPDGAT ATKPKPPPIG PKRGSKVKI LRRESYWFKN VGSVVAVDQD PKTRYPVVVR FAKVNYANIS TNNYALDEVE EVAA

UniProtKB: Photosystem I reaction center subunit IV A, chloroplastic

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Macromolecule #10: Photosystem I reaction center subunit III, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.203125 KDa
SequenceString: MSLTIPANLV LNPRSNKSLT QSVPKSSARF VCSDDKSSSS TPQSMKAFSA AVALSSILLS APMPAVADIS GLTPCKDSKQ FAKREKQQI KKLESSLKLY APESAPALAL NAQIEKTKRR FDNYGKYGLL CGSDGLPHLI VNGDQRHWGE FITPGILFLY I AGWIGWVG ...String:
MSLTIPANLV LNPRSNKSLT QSVPKSSARF VCSDDKSSSS TPQSMKAFSA AVALSSILLS APMPAVADIS GLTPCKDSKQ FAKREKQQI KKLESSLKLY APESAPALAL NAQIEKTKRR FDNYGKYGLL CGSDGLPHLI VNGDQRHWGE FITPGILFLY I AGWIGWVG RSYLIAISGE KKPAMKEIII DVPLASRIIF RGFIWPVAAY REFLNGDLIA KDV

UniProtKB: Photosystem I reaction center subunit III, chloroplastic

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Macromolecule #11: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.103271 KDa
SequenceString:
MATSASALLS PTTFSTAISH KNPNSISFHG LRPLRLGGSS SALPKLSTTG RKSSSAVVRA ELSPSIVISL STGLSLFLGR FVFFNFQRE NVAKQGLPEQ NGKTHFEAGD DRAKEYVSLL KSNDPIGFNI VDVLAWGSIG HIVAYYILAT SSNGYDPSFF G

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #12: Photosystem I reaction center subunit VI-2, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI-2, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.291522 KDa
SequenceString:
MASFATIAAV QPSAAVKGLG GSSLAGAKLF IKPSRQSFKT KSTRAGAVVA KYGDKSVYFD LEDLGNTTGQ WDVYGSDAPS PYNPLQSKF FETFAAPFTK RGLLLKFLIL GGGSLLTYVS ANSTGDVLPI KRGPQEPPKL GPRGKL

UniProtKB: Photosystem I reaction center subunit VI-2, chloroplastic

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Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 4.137024 KDa
SequenceString:
MTTFNNLPSI FVPLVGLVFP AIAMASLFLH IQKNKIF

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 5.011897 KDa
SequenceString:
MRDLKTYLSV APVLSTLWFG SLAGLLIEIN RLFPDALTFP FFSF

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #15: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.219431 KDa
SequenceString:
MASTMMTTLP QFNGLRATKI SAAPVQGLAS VQPMRRKGNG ALGAKCDFIG SSTNLIMVTS TTLMLFAGRF GLAPSANRKA TAGLRLEAR DSGLQTGDPA GFTLADTLAC GTVGHIIGVG VVLGLKNIGA I

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

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Macromolecule #16: Photosystem I reaction center subunit XI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit XI, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.070557 KDa
SequenceString: MAASASPMAS QLRSSFSSAS LSQRLAVPKG ISGAPFGVSP TKRVSSFTVR AVKSDKTTFQ VVQPINGDPF IGSLETPVTS SPLIAWYLS NLPGYRTAVN PLLRGVEVGL AHGFFLVGPF VKAGPLRNTA YAGSAGSLAA AGLVVILSMC LTIYGISSFK E GEPSIAPS ...String:
MAASASPMAS QLRSSFSSAS LSQRLAVPKG ISGAPFGVSP TKRVSSFTVR AVKSDKTTFQ VVQPINGDPF IGSLETPVTS SPLIAWYLS NLPGYRTAVN PLLRGVEVGL AHGFFLVGPF VKAGPLRNTA YAGSAGSLAA AGLVVILSMC LTIYGISSFK E GEPSIAPS LTLTGRKKQP DQLQTADGWA KFTGGFFFGG ISGVTWAYFL LYVLDLPYFV K

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

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Macromolecule #17: Photosystem I reaction center subunit N, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit N, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 18.451064 KDa
SequenceString:
MAAMNSSVLT CSYAIAGSGS VELNQKVGLV NSSVGFGQKK QMIMPVIKAQ RVVGDDVDGS NGRRSAMVFL AATLFSTAAV SASANAGVI DEYLERSKTN KELNDKKRLA TSGANFARAF TVQFGSCKFP ENFTGCQDLA KQKKVPFISE DIALECEGKD K YKCGSNVF WKW

UniProtKB: Photosystem I reaction center subunit N, chloroplastic

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Macromolecule #18: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 18 / Number of copies: 9 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 117 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 20 / Number of copies: 29 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #21: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 21 / Number of copies: 3 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #22: Lutein

MacromoleculeName: Lutein / type: ligand / ID: 22 / Number of copies: 8 / Formula: A1LXP
Molecular weightTheoretical: 568.871 Da

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 23 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #26: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 26 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #27: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 27 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #28: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 28 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #29: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 29 / 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 #30: water

MacromoleculeName: water / type: ligand / ID: 30 / Number of copies: 480 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMBis-TrisBis(2-hydroxyethyl)iminotris(hydroxymethyl)methane
0.05 %DDMn-Dodecyl-a-D-maltoside

Details: 25mM Bis-Tris, 0.05% a-DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with Cs corrector
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8764 / Average exposure time: 1.651 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1629453
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
In silico model: 3D initial reference created using the Ab-initio program in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.2) / Number images used: 148985
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.2)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8j7b


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 40.0832
Output model

PDB-9wls:
PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method

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