[English] 日本語
Yorodumi
- EMDB-12227: Photosystem I of a temperature sensitive mutant Chlamydomonas rei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12227
TitlePhotosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii
Map data
Sample
  • Complex: Photosystem I of temperature sensitive Chlamydomonas reinhardtii
    • Protein or peptide: x 18 types
  • Ligand: x 25 types
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 / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / 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 center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / 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 VIII / PSI subunit V / 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 V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center ...Photosystem I reaction center subunit VIII / PSI subunit V / 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 V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / 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 / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsCaspy I / Nelson N
Funding support Israel, 2 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
German-Israeli Foundation for Research and DevelopmentG-1483-207/2018 Israel
CitationJournal: Commun Biol / Year: 2021
Title: Dimeric and high-resolution structures of Chlamydomonas Photosystem I from a temperature-sensitive Photosystem II mutant.
Authors: Ido Caspy / Tom Schwartz / Vinzenz Bayro-Kaiser / Mariia Fadeeva / Amit Kessel / Nir Ben-Tal / Nathan Nelson /
Abstract: Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity ...Water molecules play a pivotal functional role in photosynthesis, primarily as the substrate for Photosystem II (PSII). However, their importance and contribution to Photosystem I (PSI) activity remains obscure. Using a high-resolution cryogenic electron microscopy (cryo-EM) PSI structure from a Chlamydomonas reinhardtii temperature-sensitive photoautotrophic PSII mutant (TSP4), a conserved network of water molecules - dating back to cyanobacteria - was uncovered, mainly in the vicinity of the electron transport chain (ETC). The high-resolution structure illustrated that the water molecules served as a ligand in every chlorophyll that was missing a fifth magnesium coordination in the PSI core and in the light-harvesting complexes (LHC). The asymmetric distribution of the water molecules near the ETC branches modulated their electrostatic landscape, distinctly in the space between the quinones and FX. The data also disclosed the first observation of eukaryotic PSI oligomerisation through a low-resolution PSI dimer that was comprised of PSI-10LHC and PSI-8LHC.
History
DepositionJan 19, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing 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-7blx
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12227.png

Downloads & links

-
Map

FileDownload / File: emd_12227.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.827 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.017
Minimum - Maximum-0.03777304 - 0.060399882
Average (Standard dev.)0.00018954901 (±0.0047281384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8270.8270.827
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z264.640264.640264.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0380.0600.000

-
Supplemental data

-
Sample components

+
Entire : Photosystem I of temperature sensitive Chlamydomonas reinhardtii

EntireName: Photosystem I of temperature sensitive Chlamydomonas reinhardtii
Components
  • Complex: Photosystem I of temperature sensitive Chlamydomonas reinhardtii
    • 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 V, chloroplastic
    • 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 psaK, chloroplastic
    • Protein or peptide: PSI subunit V
    • 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
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: OCTANOIC ACID (CAPRYLIC ACID)
  • Ligand: LAURIC ACID
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIACYL GLYCEROLDiglyceride
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CALCIUM IONCalcium
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • 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: SPHINGOSINE
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: CHLOROPHYLL B
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
  • Ligand: water

+
Supramolecule #1: Photosystem I of temperature sensitive Chlamydomonas reinhardtii

SupramoleculeName: Photosystem I of temperature sensitive Chlamydomonas reinhardtii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 890 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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 82.121938 KDa
SequenceString: KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLSG MYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL YTTAIGGLVM A AAMFFAGW ...String:
KKVKIAVDRN PVETSFEKWA KPGHFSRTLS KGPNTTTWIW NLHADAHDFD SHTSDLEEIS RKVFSAHFGQ LGIIFIWLSG MYFHGARFS NYEAWLSDPT HIKPSAQVVW PIVGQEILNG DVGGGFQGIQ ITSGFFQLWR ASGITSELQL YTTAIGGLVM A AAMFFAGW FHYHKAAPKL EWFQNVESML NHHLGGLLGL GSLAWAGHQI HVSLPVNKLL DAGVDPKEIP LPHDLLLNRA IM ADLYPSF AKGIAPFFTL NWSEYSDFLT FKGGLNPVTG GLWLSDTAHH HVAIAVLFLV AGHMYRTNWG IGHSMKEILE AHR GPFTGE GHVGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHTW IGGFCIVGAG AHAA IFMVR DYDPTNNYNN LLDRVIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQPVFAQ WIQNT HFLA PQLTAPNALA ATSLTWGGDL VAVGGKVAMM PISLGTSDFM VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGTVT ASGVSHITGG NFAQSANTIN GWLRDFL WA QSSQVIQSYG SALSAYGLIF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSITQ GRAVGVAH Y 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 smithii (plant)
Molecular weightTheoretical: 81.996016 KDa
SequenceString: ATKLFPKFSQ GLAQDPTTRR IWYGLAMAHD FESHDGMTEE NLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEQWVTD PVHIRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFAGWLHLQP N FQPSLSWF ...String:
ATKLFPKFSQ GLAQDPTTRR IWYGLAMAHD FESHDGMTEE NLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEQWVTD PVHIRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFAGWLHLQP N FQPSLSWF KDAESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGQHVG WDNFLSVLPH PQGLTPFFTG NWAAYAQSPD TA SHVFGTA QGSGQAILTF LGGFHPQTQS LWLTDMAHHH LAIAVIFIVA GHMYRTNFGI GHRMQAILEA HTPPSGSLGA GHK GLFDTV NNSLHFQLGL ALASVGTITS LVAQHMYSLP PYAFQAIDFT TQAALYTHHQ YIAGFIMCGA FAHGAIFFIR DYDP EQNKG NVLARMLDHK EALISHLSWV SLFLGFHTLG LYVHNDVMQA FGTPEKQILI EPVFAQWIQA AHGKALYGFD FLLSS KTSA AFANGQSLWL PGWLDAINNN QNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAY DAFYLAVFWM LNTIGWVTFY WHWKHLTLWQ GNVAQFDESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWTFLF GHLIYATGFM FLISWRGYWQ ELIETLVWAH EKTPLANLVY WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG RF

+
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: 8.73813 KDa
SequenceString:
AHIVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKASQMAS APRTEDCVGC KRCETACPTD FLSVRVYLGS ESTRSMGLSY

+
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: 16.152684 KDa
SequenceString:
WTVPTLNPDT PSPIFGGSTG GLLRKAQTEE FYVITWEAKK EQIFEMPTGG AAIMRQGPNL LKFGKKEQCL ALTTQLRNKF KLTP(SNC)FYRV FPDGKVQYLH PADGVYPEKV NAGRVGANQN MRRIGQNVNP IKVKFSGRMM SPAEI

+
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: 7.021877 KDa
SequenceString:
EVGPKRGSLV KILRPESYWF NQVGKVVSVD QSGVRYPVVV RFENQNYAGV TTNNYALDEV VAA

+
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: 17.957773 KDa
SequenceString:
DIAGLTPCSE SKAYAKLEKK ELKTLEKRLK QYEADSAPAV ALKATMERTK ARFANYAKAG LLCGNDGLPH LIADPGLALK YGHAGEVFI PTFGFLYVAG YIGYVGRQYL IAVKGEAKPT DKEIIIDVPL ATKLAWQGAG WPLAAVQELQ RGTLLEKEEN I TVSPR

+
Macromolecule #7: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.572677 KDa
SequenceString:
LDPQIVISGS TAAFLAIGRF VFLGYQRREA NFDSTVGPKT TGATYFDDLQ KNSTIFATND PAGFNIIDVA GWGALGHAVG FAVLAINSL QG

+
Macromolecule #8: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.970731 KDa
SequenceString:
PFVPPSWAPS VFVPLTGLVL PAIAMATLFV YIEKEAP

+
Macromolecule #9: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.516257 KDa
SequenceString:
MKDFTTYLST APVIATIWFT FTAGLLIEIN RYFPDPLVF

+
Macromolecule #10: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 8.146467 KDa
SequenceString:
FIGSSTNLIM VASTTATLAA ARFGLAPTVK KNTTAGLKLV DSKNSAGVIS NDPAGFTIVD VLAMGAAGHG LGVGIVLGLK GIGA

+
Macromolecule #11: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 12.944871 KDa
SequenceString:
GMLETPVTSA PIVATYLSNL PAYRTGVAPV LRGVEIGLAH GFLLAGPFIK LGPLRNVPET AEIAGSLSAA GLVLILALCL SIYGSAQFQ STVARDPLFS ADGWSEFAAG FLVGGEAGVA WAYVCTQ

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.368023 KDa
SequenceString: KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP ...String:
KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP IAALGEHLAN PWGANFATNG ISVPFF

+
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 smithii (plant)
Molecular weightTheoretical: 23.689025 KDa
SequenceString: LYVGASQSSL AYLDGSLPGD FGFDPLGLLD PVNSGGFIEP KWLQYSEVIH ARWAMLGAAG CIAPEVLGAA GLIPDATNIK WFESGVIPP AGSYNGYWAD PYTIFFVEIV AMQFAELRRL QDFRYPGSMG QQYFLGLEAI FKGSGDAAYP GGPFFNLFNL G KTEAAMKE ...String:
LYVGASQSSL AYLDGSLPGD FGFDPLGLLD PVNSGGFIEP KWLQYSEVIH ARWAMLGAAG CIAPEVLGAA GLIPDATNIK WFESGVIPP AGSYNGYWAD PYTIFFVEIV AMQFAELRRL QDFRYPGSMG QQYFLGLEAI FKGSGDAAYP GGPFFNLFNL G KTEAAMKE LKLKEIKNGR LAMLAMLGYG AQAVMTGKGP FQNLVEHLAD PVNNNILTNF G

+
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 smithii (plant)
Molecular weightTheoretical: 23.304396 KDa
SequenceString: VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL ...String:
VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL AMIACLGFAA QYAATGKGPL DNLADHLADP NHVNFATNGV SIPIA

+
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: 23.293613 KDa
SequenceString: RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK ...String:
RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK NGRLAMLAFL GFVAQKYATG AGPVDNLAAH LKDPWHVNYA TNGVSLPFL

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 23.018188 KDa
SequenceString: DAALPSWMPG ADLPGYLNGT LPGDFGFDPL YLGQDPVKLK WYAQAELMNA RFAMLAVAGI LVPELLSNIG FSWPGAGVAW YDAGKFEYF APASSLFGVQ MLLFAWVEIR RYQDFVKPGS ANQDPIFTNN KLPDGNEPGY PGGIFDPFGW SKGDIKSLKL K EIKNGRLA ...String:
DAALPSWMPG ADLPGYLNGT LPGDFGFDPL YLGQDPVKLK WYAQAELMNA RFAMLAVAGI LVPELLSNIG FSWPGAGVAW YDAGKFEYF APASSLFGVQ MLLFAWVEIR RYQDFVKPGS ANQDPIFTNN KLPDGNEPGY PGGIFDPFGW SKGDIKSLKL K EIKNGRLA MLAFAGFIGQ AYTTGTTPLK NLSTHLADPW STTVWQNDLA RL

+
Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 25.122805 KDa
SequenceString: DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVLV QEIVKPDVYF YEAGLPQNLP EPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPFGFSKGNL KELQTKEIKN G RLAMIAYM ...String:
DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVLV QEIVKPDVYF YEAGLPQNLP EPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPFGFSKGNL KELQTKEIKN G RLAMIAYM AFILQAQATG KGPLAALSAH LSNPFGNNIL KNIGTCTVPH SVDVQGLTIP LTCLWPGSQ

+
Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 24.937922 KDa
SequenceString: RPLWLPGSTP PAHLKGDLPG DFGFDPLGLG ANAESLKWFK ESELVHSRWA MAAVAGILVQ EIVRPDVFWY NAGKEVESPL GPLGLLAVE FFLMHWVEVR RWQDLRKPGS VDQDPIFSQY KLPPHEVGYP GGVFAPFIPG DLAELKVKEI KNGRLAMLAF V GFVMAAQV ...String:
RPLWLPGSTP PAHLKGDLPG DFGFDPLGLG ANAESLKWFK ESELVHSRWA MAAVAGILVQ EIVRPDVFWY NAGKEVESPL GPLGLLAVE FFLMHWVEVR RWQDLRKPGS VDQDPIFSQY KLPPHEVGYP GGVFAPFIPG DLAELKVKEI KNGRLAMLAF V GFVMAAQV TGKGPIAALQ EHLADPWGTT IFSKAAVVPG QAVAPPCKIP ASVSYKGIEI PTPCFLQGLW P

+
Macromolecule #19: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 19 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

+
Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 197 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #21: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 21 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

+
Macromolecule #22: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 22 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 31 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 14 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #25: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate

MacromoleculeName: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
type: ligand / ID: 25 / Number of copies: 3 / Formula: NKP
Molecular weightTheoretical: 436.52 Da
Chemical component information

ChemComp-NKP:
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate

+
Macromolecule #26: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 26 / Number of copies: 7 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #27: OCTANOIC ACID (CAPRYLIC ACID)

MacromoleculeName: OCTANOIC ACID (CAPRYLIC ACID) / type: ligand / ID: 27 / Number of copies: 1 / Formula: OCA
Molecular weightTheoretical: 144.211 Da
Chemical component information

ChemComp-OCA:
OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid

+
Macromolecule #28: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 28 / Number of copies: 1 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID / Lauric acid

+
Macromolecule #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #30: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 30 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL / Diglyceride

+
Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #32: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #33: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 33 / Number of copies: 1 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol / Β-Cryptoxanthin

+
Macromolecule #34: (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: 34 / Number of copies: 3 / 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 #35: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 35 / Number of copies: 3 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / Sphingosine

+
Macromolecule #36: (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: 36 / Number of copies: 17 / 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 / Lutein

+
Macromolecule #37: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 37 / Number of copies: 20 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

+
Macromolecule #38: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 38 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #39: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl...

MacromoleculeName: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one
type: ligand / ID: 39 / Number of copies: 1 / Formula: QTB
Molecular weightTheoretical: 260.414 Da
Chemical component information

ChemComp-QTB:
(3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one

+
Macromolecule #40: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 40 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

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

+
Macromolecule #41: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 41 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

+
Macromolecule #42: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypro...

MacromoleculeName: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
type: ligand / ID: 42 / Number of copies: 1 / Formula: LPX
Molecular weightTheoretical: 453.55 Da
Chemical component information

ChemComp-LPX:
(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate

+
Macromolecule #43: water

MacromoleculeName: water / type: ligand / ID: 43 / Number of copies: 331 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 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 / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12418 / Average electron dose: 46.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1208518
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ijo

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationNumber classes: 6 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 17311
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6jo5

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7blx:
Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii

+
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