[English] 日本語
Yorodumi
- EMDB-10746: Plant PSI-ferredoxin supercomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10746
TitlePlant PSI-ferredoxin supercomplex
Map data
Sample
  • Complex: Pea Photosystem I in complex with Ferredoxin
    • Protein or peptide: x 17 types
  • Ligand: x 16 types
KeywordsMembrane complex / photosystem I / ferredoxin / light harvesting / excitation transfer / PHOTOSYNTHESIS
Function / homology
Function and homology information


response to low light intensity stimulus / response to high light intensity / 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 ...response to low light intensity stimulus / response to high light intensity / 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 / chloroplast stroma / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK ...Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Electron transport accessory-like domain superfamily / 2Fe-2S iron-sulfur cluster binding 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
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI subunit V / PSI-K / Ferredoxin-1, chloroplastic ...Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II, chloroplastic / PSI subunit V / PSI-K / Ferredoxin-1, chloroplastic / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsCaspy I / Nelson N
Funding support Israel, 2 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
German-Israeli Foundation for Research and Development1483 Israel
CitationJournal: Nat Plants / Year: 2020
Title: The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin.
Authors: Ido Caspy / Anna Borovikova-Sheinker / Daniel Klaiman / Yoel Shkolnisky / Nathan Nelson /
Abstract: The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the ...The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes-photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the fundamental components of oxygenic photosynthesis, providing oxygen, food and an energy source for most living organisms on Earth. Currently, high-resolution crystal structures of these complexes from various organisms are available. The crystal structures of megadalton complexes have revealed excitation transfer and electron-transport pathways within the various complexes. PSI is defined as plastocyanin-ferredoxin oxidoreductase but a high-resolution structure of the entire triple supercomplex is not available. Here, using a new cryo-electron microscopy technique, we solve the structure of native plant PSI in complex with its electron donor plastocyanin and the electron acceptor ferredoxin. We reveal all of the contact sites and the modes of interaction between the interacting electron carriers and PSI.
History
DepositionMar 12, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6yac
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10746.png

Downloads & links

-
Map

FileDownload / File: emd_10746.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 330 pix.
= 358.05 Å		1.09 Å/pix.
x 330 pix.
= 358.05 Å		1.09 Å/pix.
x 330 pix.
= 358.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0131 / Movie #1: 0.017
Minimum - Maximum-0.059374478 - 0.11133092
Average (Standard dev.)-0.00005273846 (±0.0043332344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 358.05002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z358.050358.050358.050
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0590.111-0.000

-
Supplemental data

-
Sample components

+
Entire : Pea Photosystem I in complex with Ferredoxin

EntireName: Pea Photosystem I in complex with Ferredoxin
Components
  • Complex: Pea Photosystem I in complex with Ferredoxin
    • 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: PsaD
    • Protein or peptide: PsaE
    • Protein or peptide: PsaF
    • Protein or peptide: PsaG
    • Protein or peptide: PsaH
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit X psaK
    • Protein or peptide: PsaL
    • Protein or peptide: Lhca1
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 3, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein P4, chloroplastic
    • Protein or peptide: Ferredoxin-1, 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~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: water

+
Supramolecule #1: Pea Photosystem I in complex with Ferredoxin

SupramoleculeName: Pea Photosystem I in complex with Ferredoxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 660 KDa

+
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: Pisum sativum (garden pea)
Molecular weightTheoretical: 82.571484 KDa
SequenceString: PEVKILVDRD PIKTSFEQWA KPGHFSRTIA KGPDTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LSIIFLWLSG MYFHGARFS NYEAWLNDPT HIRPSAQVVW PIVGQEILNG DVGGGFRGIQ ITSGFFQIWR ASGITSELQL YCTAIGALVF A ALMLFAGW ...String:
PEVKILVDRD PIKTSFEQWA KPGHFSRTIA KGPDTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LSIIFLWLSG MYFHGARFS NYEAWLNDPT HIRPSAQVVW PIVGQEILNG DVGGGFRGIQ ITSGFFQIWR ASGITSELQL YCTAIGALVF A ALMLFAGW FHYHKAAPKL VWFQDVESML NHHLAGLLGL GSLSWAGHQV HVSLPINQFL NAGVDPKEIP LPHEFILNRD LL AQLYPSF AEGATPFFTL NWSKYADFLT FRGGLDPLTG GLWLTDIAHH HLAIAILFLI AGHMYRTNWG IGHGIKDILE AHK GPFTGQ GHKGLYEILT TSWHAQLSIN LAMLGSLTII VAHHMYAMPP YPYLATDYGT QLSLFTHHMW IGGFLIVGAA AHAA IFMVR DYDPTTRYND LLDRVLRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQPVFAQ WIQNT HALA PGTTAPGATT STSLTWGGGD LVSVGGKVAL LPIPLGTADF LVHHIHAFTI HVTVLILLKG VLFARSSRLI PDKANL GFR FPCDGPGRGG TCQVSAWDHV FLGLFWMYNA ISVVIFHFSW KMQSDVWGSI NDQGVVTHIT GGNFAQSSIT INGWLRD FL WAQASQVIQS YGSSLSAYGL FFLGAHFVWA FSLMFLFSGR GYWQELIESI VWAHNKLKVA PATQPRALSI VQGRAVGV T HYLLGGIATT WAFFLARIIA VG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

+
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: Pisum sativum (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

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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

UniProtKB: Photosystem I iron-sulfur center

+
Macromolecule #4: PsaD

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

+
Macromolecule #5: PsaE

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

+
Macromolecule #6: PsaF

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

+
Macromolecule #7: PsaG

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

+
Macromolecule #8: PsaH

MacromoleculeName: PsaH / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 9.491742 KDa
SequenceString:
VYFDLEDLGN TTGQWDLYGS DAPSPYNSLQ SKFFETFAAP FTKRGLLLKF LILGGGSTLA YFSATASGDI LPIKKGPQLP PQLGPRLG

+
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: Pisum sativum (garden pea)
Molecular weightTheoretical: 3.409198 KDa
SequenceString:
INLPSLFVPL VGLLFPAVAM ASLFLHVEKR L

UniProtKB: Photosystem I reaction center subunit VIII

+
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: Pisum sativum (garden pea)
Molecular weightTheoretical: 4.767609 KDa
SequenceString:
MRDLKTYLSV APVASTLWFA ALAGLLIEIN RFFPDALTFP FF

UniProtKB: Photosystem I reaction center subunit IX

+
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: Pisum sativum (garden pea)
Molecular weightTheoretical: 8.135471 KDa
SequenceString:
FIGSPTNLIM VTSTSLMLFA GRFGLAPSAN RKATAGLKLE ARDSGLQTGD PAGFTLADTL ACGVVGHIIG VGVVLGLKNI G

UniProtKB: PSI-K

+
Macromolecule #12: PsaL

MacromoleculeName: PsaL / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 16.564977 KDa
SequenceString:
YQVVQPINGD PFIGSLETPV TSSPLVAWYL SNLPGYRTAV NPLLRGIEVG LAHGFLLVGP FVKAGPLRNT EIAGQAGSLA AGGLVVILS ICLTIYGISS FNEGDPSTAP SLTLTGRKKQ PDQLQTADGW AKFTGGFFFG GISGVIWAFF LLYVLDLP

+
Macromolecule #13: Lhca1

MacromoleculeName: Lhca1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (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

+
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: Pisum sativum (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

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
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: Pisum sativum (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

UniProtKB: Chlorophyll a-b binding protein 3, chloroplastic

+
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: Pisum sativum (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

UniProtKB: Chlorophyll a-b binding protein P4, chloroplastic

+
Macromolecule #17: Ferredoxin-1, chloroplastic

MacromoleculeName: Ferredoxin-1, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pisum sativum (garden pea)
Molecular weightTheoretical: 10.359312 KDa
SequenceString:
ASYKVKLVTP DGTQEFECPS DVYILDHAEE VGIDLPYSCR AGSCSSCAGK VVGGEVDQSD GSFLDDEQIE AGFVLTCVAY PTSDVVIET HKEEDLTA

UniProtKB: Ferredoxin-1, chloroplastic

+
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

+
Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 141 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
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

+
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

+
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

+
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

+
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

+
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

+
Macromolecule #26: CALCIUM ION

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

+
Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
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: 7 / 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

+
Macromolecule #29: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 29 / Number of copies: 15 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
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: 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

+
Macromolecule #31: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca- ...Name: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 31 / Number of copies: 1 / Formula: C7Z
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-C7Z:
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol

+
Macromolecule #32: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 32 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 56 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3669 / Average electron dose: 1.075 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1776870
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5l8r

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 269657
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5l8r

source_name: PDB, initial_model_type: experimental model

1a70

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6yac:
Plant PSI-ferredoxin supercomplex

+
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