[English] 日本語
Yorodumi
- EMDB-9670: Structure of PSI-LHCI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9670
TitleStructure of PSI-LHCI
Map dataPSI-LHCI
Sample
  • Complex: PSI-LHCI
    • Protein or peptide: x 21 types
  • Ligand: x 10 types
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / oxidoreductase activity / metal ion binding
Similarity search - Function
: / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction center subunit V/PsaK ...: / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 XII / Photosystem I P700 chlorophyll a apoprotein A1 / PSI-J / PsaK / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic ...Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / PSI-J / PsaK / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I / Chlorophyll a-b binding protein, chloroplastic / 9 kDa polypeptide / PsaD / PsaE / PSI-F / PsaH / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsXiong P / Xiaochun Q
CitationJournal: Nat Plants / Year: 2019
Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.
Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui /
Abstract: Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an ...Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 Å resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution.
History
DepositionSep 27, 2018-
Header (metadata) releaseFeb 13, 2019-
Map releaseFeb 13, 2019-
UpdateMar 4, 2020-
Current statusMar 4, 2020Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6igz
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9670.png

Downloads & links

-
Map

FileDownload / File: emd_9670.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSI-LHCI
Voxel sizeX=Y=Z: 0.8727 Å
Density
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.060164515 - 0.18709584
Average (Standard dev.)0.0019334673 (±0.0052781226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 401.442 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.87270.87270.8727
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z401.442401.442401.442
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.0600.1870.002

-
Supplemental data

-
Sample components

+
Entire : PSI-LHCI

EntireName: PSI-LHCI
Components
  • Complex: PSI-LHCI
    • 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: PsaG
    • Protein or peptide: PsaH
    • Protein or peptide: PsaI
    • Protein or peptide: PsaJ
    • Protein or peptide: PsaK
    • Protein or peptide: PsaL
    • Protein or peptide: Lhca-a
    • Protein or peptide: Lhca-c
    • Protein or peptide: Lhca-d
    • Protein or peptide: Lhca-b
    • Protein or peptide: Lhca-g
    • Protein or peptide: Lhca-h
    • Protein or peptide: Lhca-i
    • Protein or peptide: Lhca-j
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
  • Ligand: HEPTYL 1-THIOHEXOPYRANOSIDE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CHLOROPHYLL B
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

+
Supramolecule #1: PSI-LHCI

SupramoleculeName: PSI-LHCI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Bryopsis corticulans (plant)

+
Macromolecule #1: PsaA

MacromoleculeName: PsaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 83.412336 KDa
SequenceString: MTISPPEREI KKVKVIVDRN TTDTSFEKWA KPGHFSRTLA KGPTTTTWIW NLHADAHDFD SHTSDLEDIS RKVFSAHFGQ LGIILIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELEL Y STALGGLL ...String:
MTISPPEREI KKVKVIVDRN TTDTSFEKWA KPGHFSRTLA KGPTTTTWIW NLHADAHDFD SHTSDLEDIS RKVFSAHFGQ LGIILIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELEL Y STALGGLL LASAMFFAGW FHYHKAAPKL EWFQNVESMM NHHLAGLLGL GSLGWAGHQI HLSIPINKLL DAGVDPKEIP LP HEFLLNR ELMAGLYPSF SAGLKPFFTL NWSEYSDFLT FKGGLNPING GLWLTDIAHH HLAIAVLFII AGHMYRTNWG IGH SMKEIL ESHKGPFTGA GHQGLYEILT NSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHTW IGGF CIVGA GAHAAIFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT TIQLQ PIFA QWIQSIHYAA PQLTAPTASA ATSLTWGGDI VSVGGKVAMM PISLGTSDFM VHHIHAFTIH VTALILLKGV LYSRSS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVS ESGVSHITGG NFANSAN AI NGWLRDFLWA QSSQVIQSYG SALSAYGLVF LGAHFVWAFS LMFLFSGRGY WQELIESILW AHNKLKVAPA IQPRALSI T QGRAVGVAHY IFGGIVTTWS FFLARIIAVG

+
Macromolecule #2: PsaB

MacromoleculeName: PsaB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 82.164461 KDa
SequenceString: MATKFPKFSQ GLAQDPTTRR IWFGVATAHD FESHDSITEE TLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEAWVQD PLHIRPIAH AIWDPHFGQS AVEAFTRGGA SGPVNIATSG VYQWWYTIGM RTNQDLYQGS VFLSIAAGLF LIAGWLHLQP K FQPTLSWF ...String:
MATKFPKFSQ GLAQDPTTRR IWFGVATAHD FESHDSITEE TLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEAWVQD PLHIRPIAH AIWDPHFGQS AVEAFTRGGA SGPVNIATSG VYQWWYTIGM RTNQDLYQGS VFLSIAAGLF LIAGWLHLQP K FQPTLSWF KNAESRLNHH LAGLFGVSSL AWTGHLVHVA IPESRGIHVR WDNFLTILPH PLGLKPFFTG NWSAYAQNPD TI NHIFSTN TGSGDAILTF LGGFHPQTQS LWLTDMAHHH LAIAVLFIIA GHMYRTNFGI GHSMKEILDM HTPPSGNLGA GHQ NLFDTI NNSLHFQLGL ALASAGTICS MVAQHMYSLP AYAFIASDFT TQASLYTHHQ YIAGFMLCGA FAHGAIFFIR DYDP VANKG NVLARILDHK EAIISHLSWV SLFLGFHTLG LYVHNDVMLA FGTPEKQILI EPVFAQWIQA AQGKSLYGFD FLLAS STSP AFNASQTVWL PGWLDAINNP TNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLSVFWM LNTIGWVTFY WHWKHLGIWQ GNVNQFNESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWMFLF GHLVYATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLVR WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG KFG

+
Macromolecule #3: PsaC

MacromoleculeName: PsaC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 8.880307 KDa
SequenceString:
MSHNVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAKQIA SAPRTEDCVG CKRCETACPT DFLSVRVYLG AETTRSMGLA Y

+
Macromolecule #4: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 21.733045 KDa
SequenceString: MASSMTSSRT TVLTSRPAFA GQRVCAKVVR TRVTPAKFAV RAADAEAPAE EAPKVWTPPQ LDPNTPSPIF GGSTGGLLRK AQVEEFYVI TWEAKKEQIF EMPTGGAAIM RKGPNLLKLA RKEQCLALTT QLRTKFKTDA CFYRVFPSGE VQYLHPKDGV Y PEKVNAGR ...String:
MASSMTSSRT TVLTSRPAFA GQRVCAKVVR TRVTPAKFAV RAADAEAPAE EAPKVWTPPQ LDPNTPSPIF GGSTGGLLRK AQVEEFYVI TWEAKKEQIF EMPTGGAAIM RKGPNLLKLA RKEQCLALTT QLRTKFKTDA CFYRVFPSGE VQYLHPKDGV Y PEKVNAGR EGANQNMRSI GENVNPIKVK FTGKIGPFDV

+
Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 10.096458 KDa
SequenceString:
MQFSAVRIAT SVRATPVRAA KAEPETPPPV GPKRGSRVKI LRPESYWYNR AGKVVSCDQT GIKYPVTVRF EDVNYAGVST NNFGLQEVE EL

+
Macromolecule #6: PsaF

MacromoleculeName: PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 25.129158 KDa
SequenceString: MATVFCASPL QLSSKCGLKP LKAKAPAPKA VRAVRAVSCS AENTTKNVAT TVAAAALAAV VSFGAVGEAK ADIAGLTPCS ESKAFKRRE NKEVKSLQKR MAKYEEGSAP ALALQATAER TQKRFEFYGK SGLLCGNDGL PHLIADPGLA FRYGHAGDIM I PTVLFIYM ...String:
MATVFCASPL QLSSKCGLKP LKAKAPAPKA VRAVRAVSCS AENTTKNVAT TVAAAALAAV VSFGAVGEAK ADIAGLTPCS ESKAFKRRE NKEVKSLQKR MAKYEEGSAP ALALQATAER TQKRFEFYGK SGLLCGNDGL PHLIADPGLA FRYGHAGDIM I PTVLFIYM AGYTGYAGRE YLLATRGEKK PTQKEIIIDV PLALKCVAGS AGWPLRAFND LRSGSLLEKE ENITVSPR

+
Macromolecule #7: PsaG

MacromoleculeName: PsaG / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 18.2266 KDa
SequenceString:
MAAATASLSS TLLAPCSSKQ PQPQQQHQHQ QLKCKSFSGL RPLKLNISSN NSSSSLSMSS ARRSMTCRAE LSPSLVISLS TGLSLFLGR FVFFNFQREN VAKQVPEQNG LTHFEAGDTR AKEYVSLLKS NDPVGFNIVD VLAWGSIGHI VAYYILATTS N GYDPSFF

+
Macromolecule #8: PsaH

MacromoleculeName: PsaH / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 14.40036 KDa
SequenceString:
MSVSAAKVST FVRGTPVRMS APKAKIQRAP ICTAPRAKYG ESDRYFDLDD LENTLGSWDM YGQEDQKRYP GLQNEFFERA GESLTRREA IRSVLFLGGG GALLAWGAKG ASDVTLPITV GPQKGGEKGP KGKI

+
Macromolecule #9: PsaI

MacromoleculeName: PsaI / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 3.859615 KDa
SequenceString:
MNAAYLPSIF VPLVGLVFPA IAMASAFLYI EKSAIE

+
Macromolecule #10: PsaJ

MacromoleculeName: PsaJ / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 4.744679 KDa
SequenceString:
MQNLKIYLST APVIAFIWLS LLSSLIIEVN RFFPDPLIFA F

+
Macromolecule #11: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 12.487672 KDa
SequenceString:
MTASKMSSFT GLKANTRIPS SRVVQAPVVR SRRSVKVSAD FIGSTPNLIM VASTGLCLAA GRFGLAPTVN KFATSGLNLV DKPLGLKTG DPAGFTAVDV LALGSFGHMI GIGIVLGLKA TGGL

+
Macromolecule #12: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 21.338602 KDa
SequenceString: MASVAGQCVA KPLVGSVFGK LNGMTPRAPM RSRSITVVVR AADEQKQVIQ PINGDPFIGM LETPVTSAPI VAGFLSNLPA YRTGVSPLL RGVEIGLTHG FLVAGPFIKL GPLRDAAGGA AETAGCLSGA LLVIILTACL TIYGQATFED DEPQIGVKTL S GRDIARDP ...String:
MASVAGQCVA KPLVGSVFGK LNGMTPRAPM RSRSITVVVR AADEQKQVIQ PINGDPFIGM LETPVTSAPI VAGFLSNLPA YRTGVSPLL RGVEIGLTHG FLVAGPFIKL GPLRDAAGGA AETAGCLSGA LLVIILTACL TIYGQATFED DEPQIGVKTL S GRDIARDP LQSAEGWNEF TSGWLVGGLS GVAWAYLCTQ FLPFYS

+
Macromolecule #13: Lhca-a

MacromoleculeName: Lhca-a / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 24.458012 KDa
SequenceString: MASALMQKSC VSAVVARPSR VTNRSVRVQA RPGNWLPGSE APSYLPEDLP GNYGYDPLGI SENPANMERM IECEVMNGRW AMLAVPGML AQEALGFGNW HDAPSWVYEG GSPTWFGAGM PITDIKLLAV IELVLMGGAE AMRASEPDME KRVYPGGAFD P AGFSKGNL ...String:
MASALMQKSC VSAVVARPSR VTNRSVRVQA RPGNWLPGSE APSYLPEDLP GNYGYDPLGI SENPANMERM IECEVMNGRW AMLAVPGML AQEALGFGNW HDAPSWVYEG GSPTWFGAGM PITDIKLLAV IELVLMGGAE AMRASEPDME KRVYPGGAFD P AGFSKGNL AELKLKEIKN ARLAMFAFVG FVLQYYATGK GPVQCWTEHI ADPLGANFAT NGTSLPFF

+
Macromolecule #14: Lhca-c

MacromoleculeName: Lhca-c / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 27.808264 KDa
SequenceString: MASILQQSTA FSCRSGAFTS STRSQNASRA QGARNVAVKA ADRPVWYPGN SPPEWLDGSL PGDYGYDPLG LASDPEMLKW WVQAELVHG RWAMLGTVGM IVPGVAARAG GDFPQWYDAG KVYIENSSIP FGALLMTQVL MMGWSEMMRY YEFVSPGSQG T GSFMGFTE ...String:
MASILQQSTA FSCRSGAFTS STRSQNASRA QGARNVAVKA ADRPVWYPGN SPPEWLDGSL PGDYGYDPLG LASDPEMLKW WVQAELVHG RWAMLGTVGM IVPGVAARAG GDFPQWYDAG KVYIENSSIP FGALLMTQVL MMGWSEMMRY YEFVSPGSQG T GSFMGFTE AFAGTGENGY PGGRFFDPFG LAKGDPAKLQ EYKVKEIKNG RLAMFSCLGY YAQYAATGKG PVDNWFDHIA DP FHNTCAT NGVSVPFLN

+
Macromolecule #15: Lhca-d

MacromoleculeName: Lhca-d / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 30.409689 KDa
SequenceString: MAAALLSSPI VAGVQAPKAK FVSTPKVNPT VHGLGAALKV KAEDAKVAKV DRSKDTLFFA DENSLTYLDG TLPGDYGFDP FGLLEPGNG DVGFINPSWL RYSEVIHGRF AMLGAAGCIT PEILSSLGVI PESTGIVWYR NGVIPPAGSS DVYWVDPYTL F FVEVVAMQ ...String:
MAAALLSSPI VAGVQAPKAK FVSTPKVNPT VHGLGAALKV KAEDAKVAKV DRSKDTLFFA DENSLTYLDG TLPGDYGFDP FGLLEPGNG DVGFINPSWL RYSEVIHGRF AMLGAAGCIT PEILSSLGVI PESTGIVWYR NGVIPPAGSS DVYWVDPYTL F FVEVVAMQ FAELRRLQDY RNPGSMGKQY FLGLEGVLGG SGDPSYPGGA FFNMFNLGKT EESMKVMKTR EIKNGRLAMM AM FGFGAQA ILTGKGPYQN LLDHLSDPFN NNILTNWTSV YGQL

+
Macromolecule #16: Lhca-b

MacromoleculeName: Lhca-b / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 26.575912 KDa
SequenceString: MATMMASSGV VARPAAFVGT QLPKVGVAAR PSLAVVRAAD RPIWLPGADV PEWLDGTIPG DFGYDPLKLG KDPETLKWYV QAELVHGRF AMMGLVGMLV PELLTNAGIG LPAKGTEWFN AGAAPMFAPT GVLFAMQFLL MGWAEIRRYQ DFKNPGSVNV D PIFGGKLP ...String:
MATMMASSGV VARPAAFVGT QLPKVGVAAR PSLAVVRAAD RPIWLPGADV PEWLDGTIPG DFGYDPLKLG KDPETLKWYV QAELVHGRF AMMGLVGMLV PELLTNAGIG LPAKGTEWFN AGAAPMFAPT GVLFAMQFLL MGWAEIRRYQ DFKNPGSVNV D PIFGGKLP DGNIPGYPGG IFDPFGFAKG DVDSLKLKEV KNGRLAMFAT LGFYCQAVVT GKGPIACWTS HLADPWANNV WS IELAKVI K

+
Macromolecule #17: Lhca-g

MacromoleculeName: Lhca-g / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 29.30068 KDa
SequenceString: MGAILSAGRA HVAFSSKSVQ RTGFRAVSNG SRVTMSASRP LWLPGSTPPA HLDGSMTGDF GWDPLGLGAN PEAMTWFREA ELQNGRWAM MGVFGILVQE LVKPDVFWYD APTKIDLPFN IIGIVAFQAF AMHYVEIRRW QDLRKPGSVN KDPIFSNYSL P EHEPGYPG ...String:
MGAILSAGRA HVAFSSKSVQ RTGFRAVSNG SRVTMSASRP LWLPGSTPPA HLDGSMTGDF GWDPLGLGAN PEAMTWFREA ELQNGRWAM MGVFGILVQE LVKPDVFWYD APTKIDLPFN IIGIVAFQAF AMHYVEIRRW QDLRKPGSVN KDPIFSNYSL P EHEPGYPG GIFAPFVPGD IEELKLKELK NARLSMLAFV GFVMQAQITG KGPIACWTDH LADPFGTTIF SKAVITLGGA VK PTCQIPD HVAFQGIDIP TPCFFEGFWP

+
Macromolecule #18: Lhca-h

MacromoleculeName: Lhca-h / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 28.621643 KDa
SequenceString: MAACGMATAA PFVGTQKNST LRTSSTTRPR PVNCSAADRK LWAPGVAAPS YLDGSLAGDY GWDPMGLSSD PKALAWYRQA ELVHSRWAM MGVVGILGQE ILNPDVFWYE AGLPKNLPEQ VSGLNLGGIL AFEFCMMHYV EVRRWQDYKN FGSVNEDPVF K GNSVPNEV ...String:
MAACGMATAA PFVGTQKNST LRTSSTTRPR PVNCSAADRK LWAPGVAAPS YLDGSLAGDY GWDPMGLSSD PKALAWYRQA ELVHSRWAM MGVVGILGQE ILNPDVFWYE AGLPKNLPEQ VSGLNLGGIL AFEFCMMHYV EVRRWQDYKN FGSVNEDPVF K GNSVPNEV MGYPGGIFDP FGFAKGKDIE DLKTKEIKNG RLAMVAWTGF ALQAQATGKG PIACWKDHLA DPFVSNITAN IG TCVIPDS VDVGGVNIPL YCLWPGQ

+
Macromolecule #19: Lhca-i

MacromoleculeName: Lhca-i / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 24.152645 KDa
SequenceString: MASSMLLGLT KPVVVGGARV QARRNMNVAC NAASRPMWLV GASAPDYLDG SMAGDYGYDP LGLGSDADRL AWYREAEKVN GRWAMNAVA GIVFCELLGI QTNWWEVGQN PDLPVDLPFN ALVAIEAVIM GFFEVKRYQG WKDTGMSGLN DSFPWDPLGM T SERVELAE ...String:
MASSMLLGLT KPVVVGGARV QARRNMNVAC NAASRPMWLV GASAPDYLDG SMAGDYGYDP LGLGSDADRL AWYREAEKVN GRWAMNAVA GIVFCELLGI QTNWWEVGQN PDLPVDLPFN ALVAIEAVIM GFFEVKRYQG WKDTGMSGLN DSFPWDPLGM T SERVELAE IKNGRLAMFA WTGFIAQAVV VRKGPVACLN AHLADPFGQN ILTNVLNIPE NIAQ

+
Macromolecule #20: Lhca-j

MacromoleculeName: Lhca-j / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 26.910092 KDa
SequenceString: MVFALSSFVG RPVVVGHAQP RAVRNVTRMA AERPMWYPGA TAPKHLDGSM LGDYGYDPLD LGANPDSLAW FREAELMNGR YAMLGVMGG AFVNAFGLPN WWEAGAKVDV PISLGVLIAL ELAIFAVFEY KRYEGFKKTG ECGVLSFMPF DPLNMRSEEN K LKELKNGR ...String:
MVFALSSFVG RPVVVGHAQP RAVRNVTRMA AERPMWYPGA TAPKHLDGSM LGDYGYDPLD LGANPDSLAW FREAELMNGR YAMLGVMGG AFVNAFGLPN WWEAGAKVDV PISLGVLIAL ELAIFAVFEY KRYEGFKKTG ECGVLSFMPF DPLNMRSEEN K LKELKNGR LAMVASVGFI SQYLVTGKGP VDNLKDHIVD PLHNNIYTSS VGNEVTVAIV FAAMWPMFAE AKKALGGKDD TF RAIPW

+
Macromolecule #21: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 3.505114 KDa
SequenceString:
MSISESQIFI AIFLALINGF LALRLGSTLY NS

+
Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 218 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #23: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 23 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 11 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #25: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

MacromoleculeName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
type: ligand / ID: 25 / Number of copies: 34 / Formula: 8CT
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-8CT:
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene

+
Macromolecule #26: HEPTYL 1-THIOHEXOPYRANOSIDE

MacromoleculeName: HEPTYL 1-THIOHEXOPYRANOSIDE / type: ligand / ID: 26 / Number of copies: 2 / Formula: HTG
Molecular weightTheoretical: 294.408 Da

+
Macromolecule #27: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 27 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #29: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 29 / Number of copies: 26 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

+
Macromolecule #30: (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: 30 / Number of copies: 20 / 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 / Violaxanthin

+
Macromolecule #31: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 31 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.8
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: FEI FALCON II (4k x 4k) / Average electron dose: 1.852 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59525

+
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