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- EMDB-11326: Photosystem I reduced Plastocyanin Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11326
TitlePhotosystem I reduced Plastocyanin Complex
Map data
Sample
  • Complex: Photosystem I plastocyanin complex
    • Protein or peptide: x 14 types
  • Protein or peptide: x 3 types
  • Ligand: x 16 types
Function / homology
Function and homology information


response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope ...response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / copper ion binding / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Plastocyanin / 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 / Blue (type 1) copper protein, plastocyanin-type / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Plastocyanin / 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 / Blue (type 1) copper protein, plastocyanin-type / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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 / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / 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 / Cupredoxin
Similarity search - Domain/homology
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI-K / Photosystem I iron-sulfur center / Plastocyanin, chloroplastic ...Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI-K / Photosystem I iron-sulfur center / Plastocyanin, chloroplastic / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea) / Garden pea (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsNelson N / Caspy I / Shkolnisky Y
Funding support Israel, Belgium, 4 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
Israel Science Foundation2716/17 Israel
German-Israeli Foundation for Research and DevelopmentG-1483-207/2018 Israel
European Research Council (ERC)723991 Belgium
CitationJournal: Biochem J / Year: 2021
Title: Structure of plant photosystem I-plastocyanin complex reveals strong hydrophobic interactions.
Authors: Ido Caspy / Mariia Fadeeva / Sebastian Kuhlgert / Anna Borovikova-Sheinker / Daniel Klaiman / Gal Masrati / Friedel Drepper / Nir Ben-Tal / Michael Hippler / Nathan Nelson /
Abstract: Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and ...Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB/Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared with reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover.
History
DepositionJul 7, 2020-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zoo
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11326.png

Downloads & links

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Map

FileDownload / File: emd_11326.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.308 Å
Density
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.028
Minimum - Maximum-0.07392658 - 0.17598514
Average (Standard dev.)7.799922e-05 (±0.0053951577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 392.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3081.3081.308
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z392.400392.400392.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0740.1760.000

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Supplemental data

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Sample components

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Entire : Photosystem I plastocyanin complex

EntireName: Photosystem I plastocyanin complex
Components
  • Complex: Photosystem I plastocyanin complex
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit X psaK
    • Protein or peptide: Chlorophyll a-b binding protein 6, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein P4, chloroplastic
    • Protein or peptide: Plastocyanin, chloroplastic
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: PsaD
    • Protein or peptide: Putative uncharacterized protein
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: photosystem I reaction center
    • Protein or peptide: Photosystem I reaction center subunit VIII
  • Protein or peptide: Photosystem I reaction center subunit VI,Photosystem I reaction center subunit VI
  • Protein or peptide: PsaL domain-containing protein
  • Protein or peptide: Chlorophyll a-b binding protein 3, chloroplastic
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CALCIUM ION
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • 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-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: COPPER (II) ION
  • Ligand: water

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Supramolecule #1: Photosystem I plastocyanin complex

SupramoleculeName: Photosystem I plastocyanin complex / type: complex / ID: 1 / Parent: 0
Macromolecule list: #1, #10-#11, #13-#14, #16-#17, #2-#7, #9
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightExperimental: 0.65 kDa/nm

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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: Garden pea (garden pea)
Molecular weightTheoretical: 82.717672 KDa
SequenceString: PEVKILVDRD PIKTSFEQWA KPGHFSRTIA KGPDTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LSIIFLWLSG MYFHGARFS NYEAWLNDPT (SNK)IRPSAQVVW PIVGQEILNG DVGGGFRGIQ ITSGFFQIWR ASGITSELQL YCTAIGA LV FAALMLFAGW ...String:
PEVKILVDRD PIKTSFEQWA KPGHFSRTIA KGPDTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LSIIFLWLSG MYFHGARFS NYEAWLNDPT (SNK)IRPSAQVVW PIVGQEILNG DVGGGFRGIQ ITSGFFQIWR ASGITSELQL YCTAIGA LV FAALMLFAGW FHYHKAAPKL VWFQDVESML NHHLAGLLGL GSLSWAGHQV HVSLPINQFL NAGVDPKEIP LPHEFILN R DLLAQLYPSF AEGATPFFTL NWSKYADFLT FRGGLDPLTG GLWLTDIAHH HLAIAILFLI AGHMYRTNWG IGHGIKDIL EAHKGPFTGQ GHKGLYEILT TSWHAQLSIN LAMLGSLTII VAHHMYAMPP YPYLATDYGT QLSLFTHHMW IGGFLIVGAA AHAAIFMVR DYDPTTRYND LLDRVLRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQPVFAQ W IQNTHALA PGTTAPGATT STSLTWGGGD LVSVGGKVAL LPIPLGTADF LVHHIHAFTI HVTVLILLKG VLFARSSRLI PD KANLGFR FPCDGPGRGG TCQVSAWDHV FLGLFWMYNA ISVVIFHFSW KMQSDVWGSI NDQGVVT(SNK)IT GGNFAQSSI TINGWLRDFL WAQASQVIQS YGSSLSAYGL FFLGAHFVWA FSLMFLFSGR GYWQELIESI VWAHNKLKVA PATQPRALSI VQGRAVGVT HYLLGGIATT WAFFLARIIA VG

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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: Garden pea (garden pea)
Molecular weightTheoretical: 82.381734 KDa
SequenceString: ALRFPRFSQG LAQDPTTRRI WFGIATAHDF ESHDDITEGR LYQNIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWVQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAL GPVNIAYSGV YQWWYTIGLR TNEDLYTGAI FLLFLSFISL LAGWLHLQPK W KPSVSWFK ...String:
ALRFPRFSQG LAQDPTTRRI WFGIATAHDF ESHDDITEGR LYQNIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWVQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAL GPVNIAYSGV YQWWYTIGLR TNEDLYTGAI FLLFLSFISL LAGWLHLQPK W KPSVSWFK NAESRLNHHL SGLFGVSSLA WAGHLVHVAI PGSRGEYVRW NNFLSVLPHP QGLGPLFTGQ WNLYAQNPDS SN HLFSTSQ GAGTAILTLL GGFHPQTQSL WLTDMAHHHL AIAILFLIGG HMYRTNFGIG HSIKYILEAH IPPGGRLGRG HKG LYDTIN NSIHFQLGLA LASLGVITSL VAQHMYSLPA YAFIAQDFTT QAALYTHHQY IAGFIMTGAF AHGAIFFIRD YNPE QNADN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YVHNDVMLAF GTPEKQILIE PIFAQWIQSA HGKTSYGFDV LLSST NSPA LNAGRSIWLP GWLNAINENS NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAVFWML NTIGWVTFYW HWKHITLWQG NVSQFNESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWMFLFG HLVWATGFMF LISWRGYWQE LIETLAWAHE RTPLANLIRW RDKPVALSIV QARLVGLVHF SVGYIFTY A AFLIASTSGK FG

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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: Garden pea (garden pea)
Molecular weightTheoretical: 8.860276 KDa
SequenceString:
SHSVKIYDTC IGCTQCVRAC PTDVLEMIPW GGCKAKQIAS APRTEDCVGC KRCESACPTD FLSVRVYLWH ETTRSMGLAY

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Macromolecule #4: PsaD

MacromoleculeName: PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 16.041408 KDa
SequenceString:
GFTPPELDPN TPSPIFGGST GGLLRKAQVE EFYVITWESP KEQIFEMPTG GAAIMREGPN LLKLARKEQC LALGTRLRSK YKIKYQFYR VFPSGEVQYL HPKDGVYPEK VNPGRQGVGV NFRSIGKNVS PIEVKFTGKQ PYDL

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Macromolecule #5: Putative uncharacterized protein

MacromoleculeName: Putative uncharacterized protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 7.479422 KDa
SequenceString:
PPIGPKRGAK VKILRQESYW YKGTGSVVAV DQDPNTRYPV VVRFNKVNYA NVSTNNYALD EVEEVK

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 17.137857 KDa
SequenceString:
DIAGLTPCKD SKQFAKREKQ SIKKLESSLK LYAPDSAPAL AINATIEKTK RRFDNYGKQG LLCGADGLPH LIVSGDQRHW GEFITPGIL FLYIAGWIGW VGRSYLIAIR DDKKPTQKEI IIDVPLATGL VFRGFSWPIA AYRELLNGEL VAKDV

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Macromolecule #7: photosystem I reaction center

MacromoleculeName: photosystem I reaction center / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 10.678027 KDa
SequenceString:
LNPSLVISLS TGLSLFLGRF VFFNFQRENV AKQGLPEQNG VTHFEAGDTR AKEYVSLLKS NDPVGFNIVD VLAWGSIGHI VAYYILATS SNGYDPKF

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Macromolecule #8: Photosystem I reaction center subunit VI,Photosystem I reaction c...

MacromoleculeName: Photosystem I reaction center subunit VI,Photosystem I reaction center subunit VI
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 10.043313 KDa
SequenceString:
YGDKSVYFDL EDLGNTTGQW DLYGSDAPSP YNSLQSKFFE TFAAPFTKRG LLLKFLILGG GSTLAYFSAT ASGDILPIKK GPQLPPQLG PRLG

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Macromolecule #9: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 3.409198 KDa
SequenceString:
INLPSLFVPL VGLLFPAVAM ASLFLHVEKR L

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Macromolecule #10: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 4.767609 KDa
SequenceString:
MRDLKTYLSV APVASTLWFA ALAGLLIEIN RFFPDALTFP FF

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Macromolecule #11: Photosystem I reaction center subunit X psaK

MacromoleculeName: Photosystem I reaction center subunit X psaK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 8.135471 KDa
SequenceString:
FIGSPTNLIM VTSTSLMLFA GRFGLAPSAN RKATAGLKLE ARDSGLQTGD PAGFTLADTL ACGVVGHIIG VGVVLGLKNI G

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Macromolecule #12: PsaL domain-containing protein

MacromoleculeName: PsaL domain-containing protein / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 16.86327 KDa
SequenceString:
YQVVQPINGD PFIGSLETPV TSSPLVAWYL SNLPGYRTAV NPLLRGIEVG LAHGFLLVGP FVKAGPLRNT EIAGQAGSLA AGGLVVILS ICLTIYGISS FNEGDPSTAP SLTLTGRKKQ PDQLQTADGW AKFTGGFFFG GISGVTWAFF LLYVLDLPYF

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Macromolecule #13: Chlorophyll a-b binding protein 6, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 6, chloroplastic / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 21.335439 KDa
SequenceString: DWMPGQPRPS YLDGSAPGDF GFDPLRLGEV PENLERFKES ELIHCRWAML AVPGILVPEA LGLGNWVKAQ EWAALPGGQA TYLGNPVPW GTLPTILVIE FLSIAFVEHQ RSMEKDPEKK KYPGGAFDPL GYSKDPKKFH EYKIKEVKNG RLALLAFVGI C VQQSAYPG ...String:
DWMPGQPRPS YLDGSAPGDF GFDPLRLGEV PENLERFKES ELIHCRWAML AVPGILVPEA LGLGNWVKAQ EWAALPGGQA TYLGNPVPW GTLPTILVIE FLSIAFVEHQ RSMEKDPEKK KYPGGAFDPL GYSKDPKKFH EYKIKEVKNG RLALLAFVGI C VQQSAYPG TGPLENLATH LADPWHNTIG NVLIP

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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: Garden pea (garden pea)
Molecular weightTheoretical: 22.845812 KDa
SequenceString: TVAEPDRPLW FPGSTPPPWL DGSLPGDFGF DPLGLGSDPE SLRWNVQAEL VHSRWAMLGA AGIFIPEFLT KLGILNTPSW YTAGEQEYF TDTTTLFIVE LVFIGWAEGR RWADILNPGC VNTDPIFPNN KLTGTDVGYP GGLWFDPLGW GSASPQKLKE L RTKEIKNG ...String:
TVAEPDRPLW FPGSTPPPWL DGSLPGDFGF DPLGLGSDPE SLRWNVQAEL VHSRWAMLGA AGIFIPEFLT KLGILNTPSW YTAGEQEYF TDTTTLFIVE LVFIGWAEGR RWADILNPGC VNTDPIFPNN KLTGTDVGYP GGLWFDPLGW GSASPQKLKE L RTKEIKNG RLAMLAVMGA WFQHIYTGTG PIDNLFAHLA DPGHATIFAA

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Macromolecule #15: Chlorophyll a-b binding protein 3, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 3, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 24.139521 KDa
SequenceString: RPLWFASKQS LSYLDGSLPG DYGFDPLGLS DPEGTGGFIE PRWLAYGEVI NGRFAMLGAV GAIAPEYLGK VGLIPQETAL AWFQTGVIP PAGTYNYWAD NYTLFVLEMA LMGFAEHRRF QDWAKPGSMG KQYFLGLEKG FGGSGNPAYP GGPFFNPLGF G KDEKSLKE ...String:
RPLWFASKQS LSYLDGSLPG DYGFDPLGLS DPEGTGGFIE PRWLAYGEVI NGRFAMLGAV GAIAPEYLGK VGLIPQETAL AWFQTGVIP PAGTYNYWAD NYTLFVLEMA LMGFAEHRRF QDWAKPGSMG KQYFLGLEKG FGGSGNPAYP GGPFFNPLGF G KDEKSLKE LKLKEVKNGR LAMLAILGYF IQGLVTGVGP YQNLLDHVAD PVNNNVLTSL KFH

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Macromolecule #16: Chlorophyll a-b binding protein P4, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein P4, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 21.994029 KDa
SequenceString: KKGEWLPGLA SPGYLTGSLP GDNGFDPLGL AEDPENLKWF VQAELVNGRW AMLGVAGMLL PEVFTSIGII NVPKWYDAGK EEYFASSST LFVIEFILFH YVEIRRWQDI KNPGSVNQDP IFKQYSLPAG EVGYPGGIFN PLNFAPTLEA KEKEIANGRL A MLAFLGFI ...String:
KKGEWLPGLA SPGYLTGSLP GDNGFDPLGL AEDPENLKWF VQAELVNGRW AMLGVAGMLL PEVFTSIGII NVPKWYDAGK EEYFASSST LFVIEFILFH YVEIRRWQDI KNPGSVNQDP IFKQYSLPAG EVGYPGGIFN PLNFAPTLEA KEKEIANGRL A MLAFLGFI IQHNVTGKGP FDNLLQHISD PWHNTIVQTL

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Macromolecule #17: Plastocyanin, chloroplastic

MacromoleculeName: Plastocyanin, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Garden pea (garden pea)
Molecular weightTheoretical: 10.353487 KDa
SequenceString:
VEVLLGASDG GLAFVPSSLE VSAGETIVFK NNAGFPHNVV FDEDEIPAGV DASKISMPEE DLLNAPGETY SVKLDAKGTY KFYCSPHQG AGMVGQVTVN

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Macromolecule #18: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 18 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 142 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 20 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #21: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 27 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 8 / 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: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 19 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #26: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 26 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 7 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #28: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 28 / Number of copies: 8 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #29: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 29 / Number of copies: 14 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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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: 2 / 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 #31: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 31 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #32: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 2 / 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

Concentration2.8 mg/mL
BufferpH: 7 / Details: 20mM Mes-Tris, 10mM sodium ascorbate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6129 / Average exposure time: 2.49 sec. / Average electron dose: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 359977
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yez

Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 104127
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationNumber classes: 6 / Avg.num./class: 23000 / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6yez

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 38.8
Output model

PDB-6zoo:
Photosystem I reduced Plastocyanin Complex

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