[English] 日本語
Yorodumi
- EMDB-63625: Photosystem I from the eukaryotic filamentous algae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63625
TitlePhotosystem I from the eukaryotic filamentous algae
Map datacomposite map
Sample
  • Complex: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
    • Protein or peptide: x 23 types
  • Ligand: x 9 types
KeywordsPhotosystem I / Xanthophyceae / Tribonema minus / PHOTOSYNTHESIS
Biological speciesTribonema minus (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsShao RQ / Pan XW
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2804400 China
National Natural Science Foundation of China (NSFC)32371269 China
National Natural Science Foundation of China (NSFC)32470247 China
Chinese Academy of Sciences2024kf05 China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Architecture of photosystem I-light-harvesting complex from the eukaryotic filamentous yellow-green alga Tribonema minus.
Authors: Ruiqi Shao / Yuqi Zou / Hui Shang / Yue Qiu / Zuxing Liang / Xiaodong Su / Shumeng Zhang / Mei Li / Xiaowei Pan /
Abstract: Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light ...Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light absorption capacity of the core complex. Throughout the evolution of oxygenic photoautotrophs, the core subunits of PSI have remained highly conserved, while LHCIs exhibit significant variability, presumably to adapt to diverse environments. This study presents a 2.82 Å resolution structure of PSI from the filamentous yellow-green alga Tribonema minus (Tm), a member of the class Xanthophyceae that evolved from red algae through endosymbiosis and is considered a promising candidate for biofuel production due to its high biomass and lipid content. Our structure reveals a supramolecular organization consisting of 12 core subunits and 13 LHCIs, here referred to as Xanthophyceae light-harvesting complexes (XLHs), along with the arrangement of pigments within the TmPSI-XLH supercomplex. A structural comparison between TmPSI-XLH and PSI-LHCI from various red lineages highlights distinctive features of TmPSI-XLH, suggesting that it represents a unique intermediate state in the PSI assembly process during the evolutionary transition from red algae to diatoms. Our findings advance the understanding of the molecular mechanisms responsible for energy transfer in Xanthophyceae PSI-XLH and the evolutionary adaptation of red lineages.
History
DepositionMar 4, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_63625.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4839329 - 0.8566141
Average (Standard dev.)0.0008098343 (±0.023048189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 457.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Photosystem I-Light-Harvesting Complexes from the Eukaryotic Fila...

EntireName: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
Components
  • Complex: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
    • Protein or peptide: Light-harvesting protein XLH1
    • Protein or peptide: light-harvesting protein XLH2
    • Protein or peptide: light-harvesting protein XLH3
    • Protein or peptide: light-harvesting protein XLH4
    • Protein or peptide: light-harvesting protein XLH5
    • Protein or peptide: light-harvesting protein XLH6/10
    • Protein or peptide: light-harvesting protein XLH7
    • Protein or peptide: light-harvesting protein XLH8
    • Protein or peptide: light-harvesting protein XLH9/13
    • Protein or peptide: light-harvesting protein XLH11
    • Protein or peptide: light-harvesting protein XLH12
    • 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: PsaL
    • Protein or peptide: PsaM
    • Protein or peptide: PsaR
    • Protein or peptide: PsaS
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER

+
Supramolecule #1: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Fila...

SupramoleculeName: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Tribonema minus (eukaryote)

+
Macromolecule #1: Light-harvesting protein XLH1

MacromoleculeName: Light-harvesting protein XLH1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 23.276188 KDa
SequenceString: MKVFALFALL LASVSAFMPA TPATSFVAKA GAAVKPSASS MQMSVFTDAT EAFSKDYPDF YKAGWGPTTK AERWNGRHAM FGWVLIVAT GYAKAHGLIP DPEVALNLKE WGTLSILAGP QTISNERAVV LIANVHALFM SLCAAFAPLS FQDPLLIPKG Q KDEPAAGL ...String:
MKVFALFALL LASVSAFMPA TPATSFVAKA GAAVKPSASS MQMSVFTDAT EAFSKDYPDF YKAGWGPTTK AERWNGRHAM FGWVLIVAT GYAKAHGLIP DPEVALNLKE WGTLSILAGP QTISNERAVV LIANVHALFM SLCAAFAPLS FQDPLLIPKG Q KDEPAAGL IPAIVPGLTK EAELLNGRLA MLGLVLVMGH SLATGTPFLN SVDLFLGNRL GL

+
Macromolecule #2: light-harvesting protein XLH2

MacromoleculeName: light-harvesting protein XLH2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 20.953053 KDa
SequenceString: MKAACAGVIA FAAGACAFAP ITPAVPRSST ALQAKTLEEI GGYSAETGNK PFDPLNIAAF VPPERMRQSE LHNGRVAMLA VVGWAFPEL VGKFASEDVT STHALDALSQ ADPRFWTQFI ILCGIVEANM YRHYQINNNQ YPFFDPLNLY PKDKAGQQSM E LKELKNGR ...String:
MKAACAGVIA FAAGACAFAP ITPAVPRSST ALQAKTLEEI GGYSAETGNK PFDPLNIAAF VPPERMRQSE LHNGRVAMLA VVGWAFPEL VGKFASEDVT STHALDALSQ ADPRFWTQFI ILCGIVEANM YRHYQINNNQ YPFFDPLNLY PKDKAGQQSM E LKELKNGR AAMIAFAAML AHATIPGSVP GFALPF

+
Macromolecule #3: light-harvesting protein XLH3

MacromoleculeName: light-harvesting protein XLH3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 21.701898 KDa
SequenceString: MVKSLALAAM VASAAAFAPA PFMGTRLAAV KASSSAVTMS VKEMPGVSAP LGFFDPLGFA SKASPETITK YRESELRHGR TAMLAVLGW AFTEAGCHLP VFPNAGTNPL AAAGQVPFWG WAQIFAFCGV IEFVQAKIRE RPGFQAGDYI GSGDLMDEGD D QWKSFQTK ...String:
MVKSLALAAM VASAAAFAPA PFMGTRLAAV KASSSAVTMS VKEMPGVSAP LGFFDPLGFA SKASPETITK YRESELRHGR TAMLAVLGW AFTEAGCHLP VFPNAGTNPL AAAGQVPFWG WAQIFAFCGV IEFVQAKIRE RPGFQAGDYI GSGDLMDEGD D QWKSFQTK ELNNGRLAML ASIGLIGQTA IFGQNILEQS TGKATLF

+
Macromolecule #4: light-harvesting protein XLH4

MacromoleculeName: light-harvesting protein XLH4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 24.273383 KDa
SequenceString: MKSAAVLVGA LAGASAFQAA TPLKGAVRSS SSMSMMAKSK SIPFAPQPAA LDGSLPGDVG FDPLGLTSID FDWAKWIVPA RASMRKGDE PVVVDTLYWM REAELKHCRV AMLAVVGWLA VDMGLRLPGT KYMGLSAISA HDAMVSGGNM VVMLHFALLL E LINGAAIF ...String:
MKSAAVLVGA LAGASAFQAA TPLKGAVRSS SSMSMMAKSK SIPFAPQPAA LDGSLPGDVG FDPLGLTSID FDWAKWIVPA RASMRKGDE PVVVDTLYWM REAELKHCRV AMLAVVGWLA VDMGLRLPGT KYMGLSAISA HDAMVSGGNM VVMLHFALLL E LINGAAIF AAAQGSGRKP GDFCLDPLGL AKDSAKSARY QLSEVKNGRL AMLAFSGIAT QAVLTGHSFP YLF

+
Macromolecule #5: light-harvesting protein XLH5

MacromoleculeName: light-harvesting protein XLH5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 22.618105 KDa
SequenceString: MMKAAAVLAL AGGAAAFMPA TPLAGAVKSS STMSMVASKS LPFLPKPEKL DGSLPGDVGF DPLNLSATDE LGLDLYWFRE AEVKHGRIA MLAVAGVLFC DQIGSLPGFP SGKDQMDLFW QVFAEKPNVV GAGVVAVSIL EFISGIAITA GRKDGSREAG D FNLDPFNV ...String:
MMKAAAVLAL AGGAAAFMPA TPLAGAVKSS STMSMVASKS LPFLPKPEKL DGSLPGDVGF DPLNLSATDE LGLDLYWFRE AEVKHGRIA MLAVAGVLFC DQIGSLPGFP SGKDQMDLFW QVFAEKPNVV GAGVVAVSIL EFISGIAITA GRKDGSREAG D FNLDPFNV RADPAKKATA QLQEIKNGRL AMLASMGMIA QGMTTHEGAL DNISAIWN

+
Macromolecule #6: light-harvesting protein XLH6/10

MacromoleculeName: light-harvesting protein XLH6/10 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 22.235654 KDa
SequenceString: MAMVKALAVA GLVGSAAAFT APSAFAGARV ARSAVAPSQV TMMAGKSASI PFMPKPEKLD GTVPGDVGFD PLGFSNWVNL DFLREAEIK HGRICMLAVA GWVAVDLGLH LPGDVHNVGS LEAHDTAVKF GAMSQILLWT SIFEAISTVG VVQMLNGSGR Q PGYFGFDP ...String:
MAMVKALAVA GLVGSAAAFT APSAFAGARV ARSAVAPSQV TMMAGKSASI PFMPKPEKLD GTVPGDVGFD PLGFSNWVNL DFLREAEIK HGRICMLAVA GWVAVDLGLH LPGDVHNVGS LEAHDTAVKF GAMSQILLWT SIFEAISTVG VVQMLNGSGR Q PGYFGFDP LNFSKDAASK AKLELNEIKN GRLAMLAFSG IVTQAALGND FPYF

+
Macromolecule #7: light-harvesting protein XLH7

MacromoleculeName: light-harvesting protein XLH7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 22.124809 KDa
SequenceString: MKAVACLACV GASGALAFTG APLAARAVTR TSGMTMQAEM SKSLPFLVKP KQLDGWVGNA EFDPFSLSEL LPMAFVRESE LKHGRIAML AVVGFVVSEL IHIPGEAYQA SNPVDAVNMV GAQPMLQIFA FCGFLESVFH KGKMTMMDMH ADGQTPGDFG F DPLNVSKD ...String:
MKAVACLACV GASGALAFTG APLAARAVTR TSGMTMQAEM SKSLPFLVKP KQLDGWVGNA EFDPFSLSEL LPMAFVRESE LKHGRIAML AVVGFVVSEL IHIPGEAYQA SNPVDAVNMV GAQPMLQIFA FCGFLESVFH KGKMTMMDMH ADGQTPGDFG F DPLNVSKD PAKLAQYQLS EIKNGRLAMM AISGLIHQSI ITGHGVPFN

+
Macromolecule #8: light-harvesting protein XLH8

MacromoleculeName: light-harvesting protein XLH8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 19.510305 KDa
SequenceString:
MRMVELGAGV ETGNEPWDPM GFSQMYKVNS LGINPHPQWL QESEIKHGRT AMLAFVGTLV IHAGIHIPGL DYTTDWYNSF PEFAAKNPL GLAQVMAGLT IWEGHYGTEA GLMWTGEGTR NPGELGFDPL NLMKGKSEAD VNTMKLKEIK NGRLAMIAMA G FASEHFIP GSVPLLSGQG F

+
Macromolecule #9: light-harvesting protein XLH9/13

MacromoleculeName: light-harvesting protein XLH9/13 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 23.143885 KDa
SequenceString: APPAPTQPQR RMKAAAACSL ALAAGASAFV APSSFAGSQL ARVTSAKSAL SMEFAGGLIG ADGPEPTTKN FDPLGLAEKG DVLFYREAE LKHCRLAMLA VVGMVVPNFV RLPGDIYQGV SVVEAHNAMV EKGPMVQLLF WLSLFEIITA PLTWNMQAKD R EPGDFSLD ...String:
APPAPTQPQR RMKAAAACSL ALAAGASAFV APSSFAGSQL ARVTSAKSAL SMEFAGGLIG ADGPEPTTKN FDPLGLAEKG DVLFYREAE LKHCRLAMLA VVGMVVPNFV RLPGDIYQGV SVVEAHNAMV EKGPMVQLLF WLSLFEIITA PLTWNMQAKD R EPGDFSLD PLGFCKDPEK KKRYQLSELK NGRLAMLAFS GMITQAVLTG HGFPYLY

+
Macromolecule #10: light-harvesting protein XLH11

MacromoleculeName: light-harvesting protein XLH11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 21.832453 KDa
SequenceString: MKVSAVAAGV MASGVAAFVQ PTAFAGSKLA AVASGSTMQM AAAEMSKSIP FIQRPPALTG EMPGDVGFDP LGMSENLNLG YMQAAELKH CRVAMLAVVG VLVTQFIHLP ADQFSATSPL DAIAKVPLAG HLQIFGLIAG LEMGSLNRTY DDSTDAWGKL I QDPSGAKQ ...String:
MKVSAVAAGV MASGVAAFVQ PTAFAGSKLA AVASGSTMQM AAAEMSKSIP FIQRPPALTG EMPGDVGFDP LGMSENLNLG YMQAAELKH CRVAMLAVVG VLVTQFIHLP ADQFSATSPL DAIAKVPLAG HLQIFGLIAG LEMGSLNRTY DDSTDAWGKL I QDPSGAKQ FAAKSAADKA KSQLQEIKNG RLAMIAIMGM LIQTALFGHP LP

+
Macromolecule #11: light-harvesting protein XLH12

MacromoleculeName: light-harvesting protein XLH12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 24.5389 KDa
SequenceString: TALRHAPHSK MKAAATVAAL AAVGSVSAFA PNAFTGKALS ATVKSTSALQ MADASGLVGK PFGAGSSVFD PLGLATKASD AELLRHQES EIKHGRIAML AILGMAVQER FHPFFPTSAE VANSVDAPRM ILQDYGWFWL LALWGVSVHE YDNVKHTYKP E SSTVKPYS ...String:
TALRHAPHSK MKAAATVAAL AAVGSVSAFA PNAFTGKALS ATVKSTSALQ MADASGLVGK PFGAGSSVFD PLGLATKASD AELLRHQES EIKHGRIAML AILGMAVQER FHPFFPTSAE VANSVDAPRM ILQDYGWFWL LALWGVSVHE YDNVKHTYKP E SSTVKPYS EILDGRVPGD LGFDPLELGH KEDSEYYNSM RLKEINNGRL AMIAVFGACA QEMVNGQNVF

+
Macromolecule #12: PsaA

MacromoleculeName: PsaA / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 83.163406 KDa
SequenceString: MSSKEQATKV KILVERDATA TSFEKWAKPG HFSRTLAKGP KTTTWIWNLH ADAHDFDSQT NSLEDVSRKI FSAHFGQLAV IFLWLSGMH FHGAYFSNYL AWLNNPTSIK PSAQVVWPIV GQEILNADVG GNFQGVQITS GFFQLWRAEG ITSEIQLYWT A IGALVMSG ...String:
MSSKEQATKV KILVERDATA TSFEKWAKPG HFSRTLAKGP KTTTWIWNLH ADAHDFDSQT NSLEDVSRKI FSAHFGQLAV IFLWLSGMH FHGAYFSNYL AWLNNPTSIK PSAQVVWPIV GQEILNADVG GNFQGVQITS GFFQLWRAEG ITSEIQLYWT A IGALVMSG LMLFAGWFHY HKAAPKLEWF QNAESMLNHH LSILLGLGCL SWAGHQIHVA LPINKLLDAG VAPQEIPLPH EF LVNRDLI AQLYPSFSKG LVPFFSGNWS EYSDFLTFKG GVNPVTGGLW LTDTAHHHLA LAVLFIFAGH MYRTNWGIGH SMK EMLEAH KGPFTGEGHA GLYEILTTSW HAQLAINLAM IGSLSIIVAH HMYAMPPYPY IATDYATQLS LFTHHVWIGG FCIV GGAAH GAIFMVRDYN PAKNYNNLLD RVIRHRDSII SHLNWVSIFL GFHSFGLYIH NDTMRALGRS QDMFSDTAIQ LQPIF AQWI QNLHLLAPGN TAPNALTTAS YVFGGDVVSV GSKIAIMPIK LGTADFMVHH IHAFTIHVTA LILLKGVLYA RSSKLI PDK ANLGFRFPCD GPGRGGTCQV SAWDHVFLGL FWMYNSLSIV LFHFSWKMQS DVWGSVTPTG AVSHITGGNF AQSAITI NG WLRDFLWSQA SQVIQSYGSA LSAYGLIFLG AHFIWAFSLM FLFSGRGYWQ ELIESIVWAH NKIKVAPAIQ PRALSITQ G RAVGLAHYLL GGIGTTWAFF LARIISVG

+
Macromolecule #13: PsaB

MacromoleculeName: PsaB / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 82.145773 KDa
SequenceString: MATKFPKFSQ ALAQDPTTRR IWFGIATAHD FETHDGMTEE KLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVLN PLKVKPIAH TIWDPHFGEP AIKAFTKGGA FYPVNIAYSG VYHWWYTIGM RTNNDLYLGS IGLIILSGLL LFAGWLHLQP K FSPSLSWF ...String:
MATKFPKFSQ ALAQDPTTRR IWFGIATAHD FETHDGMTEE KLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVLN PLKVKPIAH TIWDPHFGEP AIKAFTKGGA FYPVNIAYSG VYHWWYTIGM RTNNDLYLGS IGLIILSGLL LFAGWLHLQP K FSPSLSWF KNNESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGTHIG WDNFLTTPPH PDGLAPFFSG NWNVYAQNPD TA QHIFGTS QGSGSAILTF LGGFHPQTQS LWLTDMAHHH LAIAVIFIIA GHMYRTNFGI GHNMKEILDA HRPPGGRLGA GHR GLFDTI TNSLHMQLGL ALASLGVITS LTAQHMYAIS PYAFMAKDFT TQAALYTHHQ YIAGFLMVGA FAHGAIFFVR DYDP EANKN NVLARMLEHK EAIISHLSWV SLFLGFHTLG LYIHNDTVVA FGQPEKQILV EPVFAQFIQA ASGKALYGFD TLLSS SESP ATVAGSAIWL PGWLEAINSE KNDLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLSMFWM LNTIGWVTFY WHWKHVTIWQ GNPAQFNESS NYLMGWLRDY LWLNSSPLIN GYNPYGM NS LSVWAWMFLF GHLVWATGFM FLISWRGYWQ ELIETLVWAH ERTPLANLIS WKDKPVALSI VQARLVGLAH FTVGYILT Y AAFVIASTAG KFG

+
Macromolecule #14: PsaC

MacromoleculeName: PsaC / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 8.737103 KDa
SequenceString:
MSHAVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SAPRTEDCVG CKRCESACPT DFLSVRVYLG GETTRSMGLA Y

+
Macromolecule #15: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 15.405666 KDa
SequenceString:
MKLNLQPYSP IFGGSTGGWL RAAEVEEKYA ITWTSPKEQI FEMPTGGAAV MLIGENLLYL ARKEQCLALG TQLKSFKISD YKIYRIFPS GEVQFLHPKD GVFPEKVNPG RLPVGNRSFS IGKNPNPVSV KFSGQGTYES

+
Macromolecule #16: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 7.013938 KDa
SequenceString:
MDKGSKVRNL RKESYWFNEI GTVVTIDKSG IKYPALVRFT KVNYSGTNST NFSLDELQEV K

+
Macromolecule #17: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 20.668137 KDa
SequenceString:
MFKFKKLLPI FLALTITSPS IAFADVAGLI PCNESPVFTK RLNASVVKLE NRVKKYEAGS PPALALEQQI ERTKQRFDRY SKSGLLCGK DGLPHLITDG RWSHSIEFVI PGLMFLYITG WIGWVGRKYI RTVGGDTNAT EKEIIIDVPL ALKIMSTGFI W PISAWQEY ISGTLLADVS EITVSPR

+
Macromolecule #18: PsaI

MacromoleculeName: PsaI / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 3.940727 KDa
SequenceString:
MTASYLPSIL VPLVGIVFPG VAMALLFLYI EKDDIE

+
Macromolecule #19: PsaJ

MacromoleculeName: PsaJ / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 4.79257 KDa
SequenceString:
MENFLKYLST APVLLAAWMT FTAGFIIEAN RFYPDALTFP AF

+
Macromolecule #20: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 15.801178 KDa
SequenceString:
MANFIKPYNN DPFVGHLSTP VTTSAATKAF LGNLPAYRAG LSPLLRGLEV GMAHGYLLVG PFDKLGPLRN SEIALLSGFL SAVGLITIL TLCLTIYGKV SFQESTKNSS QLTNKDLLTE DGWSQFTSGF LVGAFGGAGF AYLTLLNLAL

+
Macromolecule #21: PsaM

MacromoleculeName: PsaM / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 3.249002 KDa
SequenceString:
MVTDTQVFIA LVLALISALL AIRLGTKLYV

+
Macromolecule #22: PsaR

MacromoleculeName: PsaR / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 9.267573 KDa
SequenceString:
MTEDTYWEGK APPSKVLGPV VSQIPSPALG VISLICLGVG TYSVHESNIF HTLTADTINP GYIIGSLLTP VAWGTHVASW IQKQNGK

+
Macromolecule #23: PsaS

MacromoleculeName: PsaS / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tribonema minus (eukaryote)
Molecular weightTheoretical: 11.422071 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #24: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 24 / Number of copies: 230 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 29 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #26: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

MacromoleculeName: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
type: ligand / ID: 26 / Number of copies: 45 / Formula: DD6
Molecular weightTheoretical: 582.855 Da
Chemical component information

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

+
Macromolecule #27: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 27 / Number of copies: 7 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #28: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 28 / Number of copies: 14 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #29: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17...

MacromoleculeName: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl] ...Name: (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol
type: ligand / ID: 29 / Number of copies: 5 / Formula: A1L1G
Molecular weightTheoretical: 616.87 Da

+
Macromolecule #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 30 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #31: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 31 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #32: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 32 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ly5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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