[English] 日本語
Yorodumi
- EMDB-32907: PSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32907
TitlePSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin
Map dataPSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin
Sample
  • Complex: Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.
    • Complex: Membrane supercomplex
      • Protein or peptide: x 15 types
    • Complex: ferredoxin
      • Protein or peptide: x 1 types
  • Ligand: x 6 types
Keywordsmembrane supercomplex / light harvesting / electron transport / green algae / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / 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, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / iron-sulfur cluster binding / response to light stimulus / photosynthesis / chloroplast / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / Ferredoxin [2Fe-2S], plant / 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 ...Ferredoxin, chloroplast transit peptide / Ferredoxin chloroplastic transit peptide / Ferredoxin [2Fe-2S], plant / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / 4Fe-4S dicluster domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like 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, chloroplastic / Ferredoxin, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic ...Chlorophyll a-b binding protein, chloroplastic / Ferredoxin, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, 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
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsKurisu G / Gerle C / Mitsuoka K / Kawamoto A / Tanaka H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR13M4 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Nanotechnology Platform Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2023
Title: Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin.
Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun ...Authors: Christoph Gerle / Yuko Misumi / Akihiro Kawamoto / Hideaki Tanaka / Hisako Kubota-Kawai / Ryutaro Tokutsu / Eunchul Kim / Dror Chorev / Kazuhiro Abe / Carol V Robinson / Kaoru Mitsuoka / Jun Minagawa / Genji Kurisu /
Abstract: Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural ...Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.
History
DepositionFeb 18, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32907.png

Downloads & links

-
Map

FileDownload / File: emd_32907.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.69863963 - 3.5791833
Average (Standard dev.)0.00044222616 (±0.12451174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 431.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.

EntireName: Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.
Components
  • Complex: Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.
    • Complex: Membrane supercomplex
      • 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, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit IX
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Complex: ferredoxin
      • Protein or peptide: Ferredoxin, chloroplastic
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: CHLOROPHYLL B
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

+
Supramolecule #1: Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.

SupramoleculeName: Photosystem I from Chlamydomonas reinhardtii with bound ferredoxin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Details: Membrane supercomplex purified without column use under green light conditions, stabilized by the mild detergent GDN with excess detergent removed using GraDeR and pre-plunge freezing added ferredoxin.
Molecular weightTheoretical: 785 KDa

+
Supramolecule #2: Membrane supercomplex

SupramoleculeName: Membrane supercomplex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#15
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: Wild Type strain 137c / Organelle: Chloroplast / Location in cell: Thylakoid membrane

+
Supramolecule #3: ferredoxin

SupramoleculeName: ferredoxin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #16
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Chloroplast

+
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 / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 83.239203 KDa
SequenceString: MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV ...String:
MTISTPEREA KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLS GMYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL Y TTAIGGLV MAAAMFFAGW FHYHKAAPKL EWFQNVESML NHHLGGLLGL GSLAWAGHQI HVSLPVNKLL DAGVDPKEIP LP HDLLLNR AIMADLYPSF AKGIAPFFTL NWSEYSDFLT FKGGLNPVTG GLWLSDTAHH HVAIAVLFLV AGHMYRTNWG IGH SMKEIL EAHRGPFTGE GHVGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHTW IGGF CIVGA GAHAAIFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQ PVFA QWIQNTHFLA PQLTAPNALA ATSLTWGGDL VAVGGKVAMM PISLGTSDFM VHHIHAFTIH VTVLILLKGV LFARSS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVT ASGVSHITGG NFAQSAN TI NGWLRDFLWA QSSQVIQSYG SALSAYGLIF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSI T QGRAVGVAHY LLGGIATTWS FFLARIISVG

+
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 / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 82.184266 KDa
SequenceString: MATKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHVA WQGNFEQWVT DPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG SVFLALVSAI FLFAGWLHLQ P NFQPSLSW ...String:
MATKLFPKFS QGLAQDPTTR RIWYGLAMAH DFESHDGMTE ENLYQKIFAS HFGQLSIIFL WTSGNLFHVA WQGNFEQWVT DPVHIRPIA HAIWDPHFGQ PAVEAFTRGG ASGPVNISTS GVYQWWYTIG MRTNQDLYVG SVFLALVSAI FLFAGWLHLQ P NFQPSLSW FKDAESRLNH HLSGLFGVSS LAWTGHLVHV AIPESRGQHV GWDNFLSVLP HPQGLTPFFT GNWAAYAQSP DT ASHVFGT AQGSGQAILT FLGGFHPQTQ SLWLTDMAHH HLAIAVIFIV AGHMYRTNFG IGHRMQAILE AHTPPSGSLG AGH KGLFDT VNNSLHFQLG LALASVGTIT SLVAQHMYSL PPYAFQAIDF TTQAALYTHH QYIAGFIMCG AFAHGAIFFI RDYD PEQNK GNVLARMLDH KEALISHLSW VSLFLGFHTL GLYVHNDVMQ AFGTPEKQIL IEPVFAQWIQ AAHGKALYGF DFLLS SKTS AAFANGQSLW LPGWLDAINN NQNSLFLTIG PGDFLVHHAI ALGLHTTTLI LVKGALDARG SKLMPDKKDF GYSFPC DGP GRGGTCDISA YDAFYLAVFW MLNTIGWVTF YWHWKHLTLW QGNVAQFDES STYLMGWLRD YLWLNSSQLI NGYNPFG MN SLSVWAWTFL FGHLIYATGF MFLISWRGYW QELIETLVWA HEKTPLANLV YWKDKPVALS IVQARLVGLA HFSVGYIF T YAAFLIASTS GRFG

+
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 / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.869325 KDa
SequenceString:
MAHIVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKASQMA SAPRTEDCVG CKRCETACPT DFLSVRVYLG SESTRSMGLS Y

+
Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 21.372887 KDa
SequenceString: MAVMMRTQAP AATRASSRVA VAARPAARRA VVVRAEAEAA PAAAKKAAEK PAWTVPTLNP DTPSPIFGGS TGGLLRKAQT EEFYVITWE AKKEQIFEMP TGGAAIMRQG PNLLKFGKKE QCLALTTQLR NKFKLTPCFY RVFPDGKVQY LHPADGVYPE K VNAGRVGA ...String:
MAVMMRTQAP AATRASSRVA VAARPAARRA VVVRAEAEAA PAAAKKAAEK PAWTVPTLNP DTPSPIFGGS TGGLLRKAQT EEFYVITWE AKKEQIFEMP TGGAAIMRQG PNLLKFGKKE QCLALTTQLR NKFKLTPCFY RVFPDGKVQY LHPADGVYPE K VNAGRVGA NQNMRRIGQN VNPIKVKFSG RMMSPAEI

+
Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.786395 KDa
SequenceString:
MQALSSRVNI AAKPQRAQRL VVRAEEVKAA PKKEVGPKRG SLVKILRPES YWFNQVGKVV SVDQSGVRYP VVVRFENQNY AGVTTNNYA LDEVVAAK

+
Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 24.088936 KDa
SequenceString: MALTMRNPAV KASSRVAPSS RRALRVACQA QKNETASKVG TALAASALAA AVSLSAPSAA MADIAGLTPC SESKAYAKLE KKELKTLEK RLKQYEADSA PAVALKATME RTKARFANYA KAGLLCGNDG LPHLIADPGL ALKYGHAGEV FIPTFGFLYV A GYIGYVGR ...String:
MALTMRNPAV KASSRVAPSS RRALRVACQA QKNETASKVG TALAASALAA AVSLSAPSAA MADIAGLTPC SESKAYAKLE KKELKTLEK RLKQYEADSA PAVALKATME RTKARFANYA KAGLLCGNDG LPHLIADPGL ALKYGHAGEV FIPTFGFLYV A GYIGYVGR QYLIAVKGEA KPTDKEIIID VPLATKLAWQ GAGWPLAAVQ ELQRGTLLEK EENITVSPR

+
Macromolecule #7: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.750509 KDa
SequenceString:
MKDFTTYLST APVIATIWFT FTAGLLIEIN RYFPDPLVFS F

+
Macromolecule #8: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.520697 KDa
SequenceString: MRTLSARTAA PRGFSGRRVA AVSNGSRVTM KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSL AVELLGYGNW YDAPLWAVNG GKATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF A KDSSKSGE ...String:
MRTLSARTAA PRGFSGRRVA AVSNGSRVTM KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSL AVELLGYGNW YDAPLWAVNG GKATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF A KDSSKSGE LKLKEIKNGR LAMVAFLGFV AQHAATGKGP IAALGEHLAN PWGANFATNG ISVPFF

+
Macromolecule #9: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 32.629486 KDa
SequenceString: MMLTKSAQAA FSGKVARPAK ANRARLVCRA EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQY SEVIHARWAM LGAAGCIAPE VLGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE L RRLQDFRY ...String:
MMLTKSAQAA FSGKVARPAK ANRARLVCRA EEKSIAKVDR SKDQLYVGAS QSSLAYLDGS LPGDFGFDPL GLLDPVNSGG FIEPKWLQY SEVIHARWAM LGAAGCIAPE VLGAAGLIPD ATNIKWFESG VIPPAGSYNG YWADPYTIFF VEIVAMQFAE L RRLQDFRY PGSMGQQYFL GLEAIFKGSG DAAYPGGPFF NLFNLGKTEA AMKELKLKEI KNGRLAMLAM LGYGAQAVMT GK GPFQNLV EHLADPVNNN ILTNFAGRVS GSSQPWRPHG WWRRRYRSVA ALALIRNRSV C

+
Macromolecule #10: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 26.248869 KDa
SequenceString: MALSMIAQRR AGAFSARQAP RAVRAQAAVR PVWFPGNPPP AHLDGSLAGD YGFDPLFLGQ EPQTLKWYVQ AELVHGRFAM LGAAGIILT SIGAKVGLGF PEWYDAGKVV VEKNNIDFPT LMVIQFYLMG WAETKRWYDF KNPGSQADGS FLGFTEEFKG L ENGYPGGR ...String:
MALSMIAQRR AGAFSARQAP RAVRAQAAVR PVWFPGNPPP AHLDGSLAGD YGFDPLFLGQ EPQTLKWYVQ AELVHGRFAM LGAAGIILT SIGAKVGLGF PEWYDAGKVV VEKNNIDFPT LMVIQFYLMG WAETKRWYDF KNPGSQADGS FLGFTEEFKG L ENGYPGGR FFDPMGLSRG DAAKYQEYKQ KEVKNGRLAM IACLGFAAQY AATGKGPLDN LADHLADPNH VNFATNGVSI PI A

+
Macromolecule #11: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.948812 KDa
SequenceString: MALTMKRSGV AARSASSRKS VVTCVARQSW LPGSQIPAHL DTPAAQALAG NFGFDPLGLG KDPVALRWYQ QAELIHCRTA MAGVAGILI PGLLTKAGAL NVPEWYDAGK VAIENSFAPW GSLLAVQLFL CGFVEAKRWQ DIRKPGSQGE PGSFLGFEAS L KGTSELGY ...String:
MALTMKRSGV AARSASSRKS VVTCVARQSW LPGSQIPAHL DTPAAQALAG NFGFDPLGLG KDPVALRWYQ QAELIHCRTA MAGVAGILI PGLLTKAGAL NVPEWYDAGK VAIENSFAPW GSLLAVQLFL CGFVEAKRWQ DIRKPGSQGE PGSFLGFEAS L KGTSELGY PGGPFDPLGL SKEADKWADW KLKEVKNGRL AMLAFLGFVA QKYATGAGPV DNLAAHLKDP WHVNYATNGV SL PFL

+
Macromolecule #12: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.923205 KDa
SequenceString: MALSMRTLSA RTAAPRGFSG RRVAAVSNGS RVTMKAGNWL PGSDAPAWLP DDLPGNYGFD PLSLGKEPAS LKRFTESEVI HGRWAMLGV AGSLAVELLG YGNWYDAPLW AVNGGKATWF GIEVPFDLNA LLAFEFVAMA AAEGQRGDAG GVVYPGGAFD P LGFAKDSS ...String:
MALSMRTLSA RTAAPRGFSG RRVAAVSNGS RVTMKAGNWL PGSDAPAWLP DDLPGNYGFD PLSLGKEPAS LKRFTESEVI HGRWAMLGV AGSLAVELLG YGNWYDAPLW AVNGGKATWF GIEVPFDLNA LLAFEFVAMA AAEGQRGDAG GVVYPGGAFD P LGFAKDSS KSGELKLKEI KNGRLAMVAF LGFVAQHAAT GKGPIAALGE HLANPWGANF ATNGISVPFF

+
Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.729822 KDa
SequenceString: MAFVLAKSSA FGVAAKPVSR RSSVAVKASA VPENVKEARE WIDAWKSKSG GAKRDAALPS WMPGADLPGY LNGTLPGDFG FDPLYLGQD PVKLKWYAQA ELMNARFAML AVAGILVPEL LSNIGFSWPG AGVAWYDAGK FEYFAPASSL FGVQMLLFAW V EIRRYQDF ...String:
MAFVLAKSSA FGVAAKPVSR RSSVAVKASA VPENVKEARE WIDAWKSKSG GAKRDAALPS WMPGADLPGY LNGTLPGDFG FDPLYLGQD PVKLKWYAQA ELMNARFAML AVAGILVPEL LSNIGFSWPG AGVAWYDAGK FEYFAPASSL FGVQMLLFAW V EIRRYQDF VKPGSANQDP IFTNNKLPDG NEPGYPGGIF DPFGWSKGDI KSLKLKEIKN GRLAMLAFAG FIGQAYTTGT TP LKNLSTH LADPWSTTVW QNDLARL

+
Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.257555 KDa
SequenceString: MAALMQKSAL SRPACSTRSS RRAVVVRAAA DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVL VQEIVKPDVY FYEAGLPQNL PEPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN P EMGYPGGI ...String:
MAALMQKSAL SRPACSTRSS RRAVVVRAAA DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVL VQEIVKPDVY FYEAGLPQNL PEPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN P EMGYPGGI FDPFGFSKGN LKELQTKEIK NGRLAMIAYM AFILQAQATG KGPLAALSAH LSNPFGNNIL KNIGTCTVPH SV DVQGLTI PLTCLWPGSQ

+
Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 27.812373 KDa
SequenceString: MMLVAKNAVA ARPSARSARR SVVAKASSRP LWLPGSTPPA HLKGDLPGDF GFDPLGLGAN AESLKWFKES ELVHSRWAMA AVAGILVQE IVRPDVFWYN AGKEVESPLG PLGLLAVEFF LMHWVEVRRW QDLRKPGSVD QDPIFSQYKL PPHEVGYPGG V FAPFIPGD ...String:
MMLVAKNAVA ARPSARSARR SVVAKASSRP LWLPGSTPPA HLKGDLPGDF GFDPLGLGAN AESLKWFKES ELVHSRWAMA AVAGILVQE IVRPDVFWYN AGKEVESPLG PLGLLAVEFF LMHWVEVRRW QDLRKPGSVD QDPIFSQYKL PPHEVGYPGG V FAPFIPGD LAELKVKEIK NGRLAMLAFV GFVMAAQVTG KGPIAALQEH LADPWGTTIF SKAAVVPGQA VAPPCKIPAS VS YKGIEIP TPCFLQGLWP

+
Macromolecule #16: Ferredoxin, chloroplastic

MacromoleculeName: Ferredoxin, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 13.243989 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MAMAMRSTFA ARVGAKPAVR GARPASRMSC MAYKVTLKTP SGDKTIECPA DTYILDAAEE AGLDLPYSCR AGACSSCAGK VAAGTVDQS DQSFLDDAQM GNGFVLTCVA YPTSDCTIQT HQEEALY

+
Macromolecule #17: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 17 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

+
Macromolecule #18: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 18 / Number of copies: 188 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #19: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 19 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #20: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 20 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #21: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 21 / Number of copies: 16 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

+
Macromolecule #22: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 22 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7.0 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
25.0 mMC6H13NO4SMES
0.02 %C56H92O25GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
Details: Glow discharge on both sides at 5 mA for 90 seconds each.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 2.6 microliter of sample were applied to cryo-grids and blotted for 3.5 seconds using Whatman #1 before plunge freezing..
DetailsThe sample was monodisperse with a low level of contaminants and excess free detergent removed using the GraDeR approach.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsPreliminary grid screening was performed manually using a JEOL JEM-3000SFF microscope.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-16 / Number grids imaged: 1 / Number real images: 2646 / Average exposure time: 2.0 sec. / Average electron dose: 91.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 857909
Startup modelType of model: INSILICO MODEL
In silico model: Generated using stochastic gradient descent as implemented in cryoSPARC.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 48941
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6jo5

RefinementProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-7wzn:
PSI-LHCI from Chlamydomonas reinhardtii with bound ferredoxin

+
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