[English] 日本語
Yorodumi
- EMDB-11588: Structure of low-light grown Chlorella ohadii Photosystem I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11588
TitleStructure of low-light grown Chlorella ohadii Photosystem I
Map data
Sample
  • Complex: Photosystem I
    • Protein or peptide: x 23 types
  • Ligand: x 31 types
Keywordsphotosystem I / light stress / PHOTOSYNTHESIS
Function / homology
Function and homology information


malate transport / glutathione-disulfide reductase (NADPH) activity / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups ...malate transport / glutathione-disulfide reductase (NADPH) activity / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups / chlorophyll binding / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / glutathione metabolic process / cell redox homeostasis / chloroplast / monooxygenase activity / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / cellular response to oxidative stress / electron transfer activity / oxidoreductase activity / protein kinase activity / iron ion binding / heme binding / magnesium ion binding / mitochondrion / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / Photosystem I PsaO / PsaO transmembrane domain / Aluminum-activated malate transporter / Aluminium activated malate transporter / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic ...Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / Photosystem I PsaO / PsaO transmembrane domain / Aluminum-activated malate transporter / Aluminium activated malate transporter / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction 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 / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Electron transport accessory-like domain superfamily / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Acetyltransferase (GNAT) family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / 4Fe-4S dicluster domain / Acyl-CoA N-acyltransferase / 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 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Leucine-rich repeat domain superfamily / FAD/NAD(P)-binding domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Photosystem I reaction center subunit XI, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Glutathione reductase / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VI-chloroplastic-like / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic ...Photosystem I reaction center subunit XI, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Glutathione reductase / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VI-chloroplastic-like / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-G / PSI-K / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesChlorella ohadii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: Nat.Plants / Year: 2021
Title: Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii.
Authors: Caspy I / Neumann E / Fadeeva M / Liveanu V / Savitsky A / Frank A / Kalisman YL / Shkolnisky Y / Murik O / Treves H / Hartmann V / Nowaczyk MM / Schuhmann W / Rogner M / Willner I / Kaplan ...Authors: Caspy I / Neumann E / Fadeeva M / Liveanu V / Savitsky A / Frank A / Kalisman YL / Shkolnisky Y / Murik O / Treves H / Hartmann V / Nowaczyk MM / Schuhmann W / Rogner M / Willner I / Kaplan A / Schuster G / Nelson N / Lubitz W / Nechushtai R
History
DepositionAug 5, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zzx
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11588.png

Downloads & links

-
Map

FileDownload / File: emd_11588.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112 / Movie #1: 0.015
Minimum - Maximum-0.046150174 - 0.09148993
Average (Standard dev.)0.00014379842 (±0.0034149487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0460.0910.000

-
Supplemental data

-
Half map: #2

Fileemd_11588_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11588_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem I

EntireName: Photosystem I
Components
  • Complex: Photosystem I
    • 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 chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: PSI-F
    • Protein or peptide: Photosystem I reaction center subunit chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit VI-chloroplastic-like
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I subunit O
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Glutathione reductase
    • Protein or peptide: Lhca4
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Lhca7
    • 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: CHLOROPHYLL B
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: SPHINGOSINE
  • Ligand: beta,beta-caroten-4-one
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: ASTAXANTHIN
  • Ligand: OLEIC ACID
  • Ligand: (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one
  • Ligand: PALMITIC ACID
  • Ligand: DIACYL GLYCEROL
  • Ligand: benzene-1,3,5-triol
  • 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: Tripalmitoylglycerol
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
  • Ligand: water

+
Supramolecule #1: Photosystem I

SupramoleculeName: Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 1 MDa

+
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: Chlorella ohadii (plant)
Molecular weightTheoretical: 82.125898 KDa
SequenceString: KKVKIVVDRN PVATNFEKWA KPGHFSRTLS KGPTTTTWIW NLHADAHDFD TQTSDLEEIS RKVFSAHFGQ LGIIFIWLSG MYFHGARFS NYEAWLTDPT HIKPSAQVVW PIVGQEILNA DVGGGFQGLQ ITSGFFQLWR AAGITSELQL YTTAIGALVM A AAMFFAGW ...String:
KKVKIVVDRN PVATNFEKWA KPGHFSRTLS KGPTTTTWIW NLHADAHDFD TQTSDLEEIS RKVFSAHFGQ LGIIFIWLSG MYFHGARFS NYEAWLTDPT HIKPSAQVVW PIVGQEILNA DVGGGFQGLQ ITSGFFQLWR AAGITSELQL YTTAIGALVM A AAMFFAGW FHYHKAAPKL EWFQNVESML NHHLGGLLGL GSLAWAGHQI HVSLPINKLL DAGVDPKEIP LPHEFTLNPE LM AQLYPSF SKGLAPFFTL DWAQYSDFLT FQGGLNPVTG GLWLTDTVHH HLAIAVLFLI AGHQYRTNWG IGSSLKEILE AHK GPFTGE GHKGLYEILT TSWHAQLAIN LALFGSLSII VAHHMYAMPP YPYLATDYGT QLSLFTHHMW IGGFCIVGAG AHAA IFMVR DYDPTNNYNN LLDRVLRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMSAL GRPQDMFSDT AIQLQPVFAQ WVQNT HFLA PGFTAPNALA STSPSWGGDV VAVGGKVAMM PISLGTADFL VHHIHAFTIH VTVLILLKGV LYARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSI SIVIFHFSWK MQSDVWGTVS ANGVSHITGG NFAQSANTIN GWLRDFL WA QSSQVIQSYG SALSAYGLIF LGAHFVWAFS LMFLFSGRGY WQELIESIVW AHNKLKVAPA IQPRALSITQ GRAVGVAH Y LLGGIATTWS FFLARILAVG

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: Chlorella ohadii (plant)
Molecular weightTheoretical: 81.544633 KDa
SequenceString: KLFPKFSQAL AQDPTTRRIW FGIATAHDFE SHDGMTEERL YQKIFASHFG QLAIIFLWTS GNLFHVAWQG NFEQWVQDPL HIRPIAHAI WDPHFGQPAV EAFTRGGASG PVNISTSGVY QWWYTIGLRT NQELYTGSIF LLVLAALFLF AGWLHLQPAF Q PALSWFKN ...String:
KLFPKFSQAL AQDPTTRRIW FGIATAHDFE SHDGMTEERL YQKIFASHFG QLAIIFLWTS GNLFHVAWQG NFEQWVQDPL HIRPIAHAI WDPHFGQPAV EAFTRGGASG PVNISTSGVY QWWYTIGLRT NQELYTGSIF LLVLAALFLF AGWLHLQPAF Q PALSWFKN AESRLNHHLA GLFGVSSLAW TGHLVHVAIP ESRGQHVGWD NFLTVLPHPA GLTPFFTGNW AAYAENPDSA SH VFNTAQG SGTAILTFLG GFHPQTQSLW LTDMAHHHLA IAVIFILAGH MYRTIFGIGH SMREILEAQT PPSGSLGAGH KGL YDTVNN SLHFQLGLAL ASVGTISSLV AQHMYSLPPY AFLAQDFTTQ AALYTHHQYI AGFIMCGAFA HGAIFFVRDY DPAQ NRGNV LARILDHKEA LISHLSWASL FLGFHTLGLY VHNDVVQAFG TPEKQILIEP VFAQWIQAAH GKTAYGFDFL LSSAT SAPS LAGQALWLPG WLQGINSDAN SLFLTIGPGD FLVHHAIALG LHTTTLILVK GALDARGSKL MPDKKDFGYS FPCDGP GRG GTCDISAWDA FYLAVFWMLN TIGWVTFYWH WKHLGIWQGN VNQFNESSTY LMGWLRDYLW LNSSQLINGY NPFGMNS LS VWAWMFLFGH LIYATGFMFL ISWRGYWQEL IETLAWAHER TPLANLVRWR DKPVALSIVQ ARLVGLTHFS VGYVLTYA A FLIASTSGKF

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: Chlorella ohadii (plant)
Molecular weightTheoretical: 8.723009 KDa
SequenceString:
SHTVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKANQIAS APRTEDCVGC KRCESACPTD FLSVRVYLGS ETTRSMGLAY

UniProtKB: Photosystem I iron-sulfur center

+
Macromolecule #4: Photosystem I reaction center subunit chloroplastic

MacromoleculeName: Photosystem I reaction center subunit chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 15.958232 KDa
SequenceString:
AFTPPTLQSD TPSPIFGGST GGLLSQAQVE EFHVITWESK KEQIFEMPTG GAAIMRQGPN LLKLARKEQC LALLTQLRTK FKIDGYIYR VFPNGEVQYL HPKDGVYPEK VNAGRSGDNT NMRRIGQNKE PVQIKFSGKI PAEF

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

+
Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 7.194105 KDa
SequenceString:
PDVGPKRGTQ VRILRPESYW FRETGKVVSV DQSGIRYPVV VRFEKVNYAG VSTNNYALDE VVAA

UniProtKB: Photosystem I reaction center subunit IV

+
Macromolecule #6: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 18.069887 KDa
SequenceString:
DVAGLTPCSE SKAFAKRKKN EVKALNKRLK NYEADSAPAL ALKATIARTE ARFDKYAKQG LLCGTDGLPH LIADPGLALR YGHAGDVFI PTIGFIYFAG WLGYAGSKYL QAVAATAKPI EKEIIIDVPL AWKLLWEGFG WPLRAFAEYK NGSLMEDDAK I TVSPR

UniProtKB: Photosystem I reaction center subunit III

+
Macromolecule #7: Photosystem I reaction center subunit chloroplastic

MacromoleculeName: Photosystem I reaction center subunit chloroplastic / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 10.326872 KDa
SequenceString:
LADVNLVVGG CTVGALALGR FVFLPFHRAS LAKAGMPKQN GMTHLQAGDA RAEEASFILK TNDPAGFTVV DVMAWGALGH AAAFYILAT SSLGLDRNPF

UniProtKB: PSI-G

+
Macromolecule #8: Photosystem I reaction center subunit VI-chloroplastic-like

MacromoleculeName: Photosystem I reaction center subunit VI-chloroplastic-like
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 10.319479 KDa
SequenceString:
KYGEESRYFD LKDLENTVGS WDMYGQEDKS RYNGLQSEFF ERAANGLSRR EYILGLVAIG GAGILAWGGK GAADVRLPTV GPQQPAQVG PRGRL

UniProtKB: Photosystem I reaction center subunit VI-chloroplastic-like

+
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: Chlorella ohadii (plant)
Molecular weightTheoretical: 4.475292 KDa
SequenceString:
MKDFTTYLST APVLTLLSVT VVAGLLIEIN RFFPDALIAA F

UniProtKB: Photosystem I reaction center subunit IX

+
Macromolecule #10: Photosystem I reaction center subunit chloroplastic

MacromoleculeName: Photosystem I reaction center subunit chloroplastic / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 8.725087 KDa
SequenceString:
YLGSTTNQIM VLSTFLPLVA GRFGLAPTST RHTNQSGIKL LPAEKSAGLV SNDPAGFNAV DVLALGALGH ILGCGIVLGL KSTGNL

UniProtKB: PSI-K

+
Macromolecule #11: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 16.501025 KDa
SequenceString:
KVQVVQPVNG DPFIGMLETP VTSSPAIAWY LSNLPAYRTG VSPLLRGVEI GLAHGYLLVG PFIKLGPLRD VENVAEIVGC INGAATVLI LTLCLAYGAV TFQGEGPQVG VKTLSGRSIP RDPLQSADGW NKFTAGFAVG GLSGAAWGYL CTQILPYY

UniProtKB: Photosystem I reaction center subunit XI, chloroplastic

+
Macromolecule #12: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 3.37606 KDa
SequenceString:
MPIADYQVFT ALFLALATGI FAVRLGVALY K

UniProtKB: Photosystem I reaction center subunit XII

+
Macromolecule #13: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 3.856674 KDa
SequenceString:
MSAQFLPSIL VPLVGLVFPA VAMASMFLYI EKEEI

UniProtKB: Photosystem I reaction center subunit VIII

+
Macromolecule #14: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 9.547967 KDa
SequenceString:
WGAYEEPLSL VAGFLGWFAP SNIKVPAFGN ESLFGAFHAS MLENLANFPQ GPALTDKFWI LMITWHLGLF LALTLGNIGQ AARKQGY

UniProtKB: Photosystem I subunit O

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

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 19.933604 KDa
SequenceString: KAGNWLPGSE TPAYLENLPA SYGFDPLGLA AEPASLARFR ESEVFHGRWA MLGAAGVLGV EVLGYGNWYD APLPLVQGGQ ATYFGASVP FDLGTLAAIE FAAMAGAESF RGAAEPEKRV YPGGAFDPMG MSKGNSKELK TKEIKNGRLA MLACLGFAAQ H AATGASPL ...String:
KAGNWLPGSE TPAYLENLPA SYGFDPLGLA AEPASLARFR ESEVFHGRWA MLGAAGVLGV EVLGYGNWYD APLPLVQGGQ ATYFGASVP FDLGTLAAIE FAAMAGAESF RGAAEPEKRV YPGGAFDPMG MSKGNSKELK TKEIKNGRLA MLACLGFAAQ H AATGASPL EALASHLANP MAVNFATNGV SLPL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #16: Glutathione reductase

MacromoleculeName: Glutathione reductase / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 26.163904 KDa
SequenceString: EGADLAKVER VAKVGGLYKN FTSGQALSYL DGTLPGDFGF DPLGLCDPEG AGGFITPEWL SYSEVIHCRW AMLGAAGFLA PEILATAGL IPATPEEAVW FRSGVIPPAG QYGKYWMDPY SLFWIEAILM NFAELKRWQD FKEPGSQSKQ YFLGLEAVFG G SGNPAYPG ...String:
EGADLAKVER VAKVGGLYKN FTSGQALSYL DGTLPGDFGF DPLGLCDPEG AGGFITPEWL SYSEVIHCRW AMLGAAGFLA PEILATAGL IPATPEEAVW FRSGVIPPAG QYGKYWMDPY SLFWIEAILM NFAELKRWQD FKEPGSQSKQ YFLGLEAVFG G SGNPAYPG GQWFNMLNLG KTPEEMKKLQ TNEIRNGRLA MIACLGCAAQ GVMTQKGPFA NLLEHLADPV SNNLLGNLAT IL K

UniProtKB: Glutathione reductase

+
Macromolecule #17: Lhca4

MacromoleculeName: Lhca4 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 23.010994 KDa
SequenceString: AGWDLSAEVP AHLAGRKDLA GNYGFDPLNL GKNPEALKWY QQAELQNGRW AMLGVAGILV QELLHSTGLG GKAADVYWFD AGNNTFWAP KETLIAISFL MFNWAELNRM QDYIKPGSNV TDPFGNKIKY VELGYPGFDP LSFSKNNFDE WKLKEIKNAR L AMLAFLGI ...String:
AGWDLSAEVP AHLAGRKDLA GNYGFDPLNL GKNPEALKWY QQAELQNGRW AMLGVAGILV QELLHSTGLG GKAADVYWFD AGNNTFWAP KETLIAISFL MFNWAELNRM QDYIKPGSNV TDPFGNKIKY VELGYPGFDP LSFSKNNFDE WKLKEIKNAR L AMLAFLGI VAQHNAQPGS PLEQLGAHLA NPWKNHFINN GVSPFLTDN

+
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: Chlorella ohadii (plant)
Molecular weightTheoretical: 25.371012 KDa
SequenceString: QRKLWFPGVA APGYLDGSMA GDRGFDPMGL GANPKMMTWY RQAELQNGRW AMLGVAGILG QEIINPAQWW YTAGMPENLP RFDSQPVNM GGILAWEFIL MHFVEVRRWQ DIRKKDSVNA DPFNPNLKVP NPELGYPGGP FDPLGFSKGN FKEAQTKEIK N GRLAMVAF ...String:
QRKLWFPGVA APGYLDGSMA GDRGFDPMGL GANPKMMTWY RQAELQNGRW AMLGVAGILG QEIINPAQWW YTAGMPENLP RFDSQPVNM GGILAWEFIL MHFVEVRRWQ DIRKKDSVNA DPFNPNLKVP NPELGYPGGP FDPLGFSKGN FKEAQTKEIK N GRLAMVAF AAFTIQAQAT GKGPLQNLTD HLSAPFSNNW TTNIGHCMVP TSVDVQGLTI PLSCLWPGQQ M

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 25.31624 KDa
SequenceString: ARANWLPGSD FPAHLENCKL PGCYGFDPLG LGANEERLAW FAESERVHCR WAMLGVAGIL VQEIVKPDVF WYTSGATVEL PFDITGLLA FELFVMHWVE SRRGYDIKKP GSMDQDPIFS NFKLPAHEPG YPGGIFAPFV PGSLEELKVK EIKNGRLAML A FIGFTMAA ...String:
ARANWLPGSD FPAHLENCKL PGCYGFDPLG LGANEERLAW FAESERVHCR WAMLGVAGIL VQEIVKPDVF WYTSGATVEL PFDITGLLA FELFVMHWVE SRRGYDIKKP GSMDQDPIFS NFKLPAHEPG YPGGIFAPFV PGSLEELKVK EIKNGRLAML A FIGFTMAA QVTGKNPLAA LREHLDNPLG TTIFSKAVVV PGQAVVPPCA IPDTIEFQGI TIPAGCFLHS LWP

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #20: Lhca7

MacromoleculeName: Lhca7 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 24.016156 KDa
SequenceString: VRELWFPGNK EVVPDYLDGS LVGDHGFDPL GLGSSPEQLS WNVHAEIFHG RLAMTGVAGI LLTSLLHKGG ADVPEWFEAG RVYLDRNPN VDFGALLFST IVMSGFVEFK RLNDIRNPGS QGSGILPEDF KGVGGPQGRT VGGPYVGGRY FDPMGLCRGS P EQTLKYKW ...String:
VRELWFPGNK EVVPDYLDGS LVGDHGFDPL GLGSSPEQLS WNVHAEIFHG RLAMTGVAGI LLTSLLHKGG ADVPEWFEAG RVYLDRNPN VDFGALLFST IVMSGFVEFK RLNDIRNPGS QGSGILPEDF KGVGGPQGRT VGGPYVGGRY FDPMGLCRGS P EQTLKYKW NEIRNGRLAM MAFLGFAAQY AATGKGPIDN LVDHVADPFH TTFVHNGVSV PFI

+
Macromolecule #21: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 23.612713 KDa
SequenceString: ATRPLWQPGV EAPKHLDGTM PGDFGFDPLN LGVNKEALNW YRNAELQNGR WAMLGVAGIV IPAELTRVGV LNVPEWAEAG KVYAESENA IPFASLLMVQ LFLFNFVEIK RWEDIKKPGS QAEPGSFLGF ESGFKGTGIS GYPGGAFNPF GLGNSSKEAM D DLKWREIR ...String:
ATRPLWQPGV EAPKHLDGTM PGDFGFDPLN LGVNKEALNW YRNAELQNGR WAMLGVAGIV IPAELTRVGV LNVPEWAEAG KVYAESENA IPFASLLMVQ LFLFNFVEIK RWEDIKKPGS QAEPGSFLGF ESGFKGTGIS GYPGGAFNPF GLGNSSKEAM D DLKWREIR NGRLAMVAFL GFLSQHAATG KGPLDNLADH LADPWGANFC SNGVSIPSAL G

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #22: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 23.618 KDa
SequenceString: RPTWYPGATP PKYLDGTMLG DYGFDPLRLG SKDKDVLKYY REGELTNGRW AMAAVAGILF TDLVGLGPWW EAGAKVESSF DLKTLIIIE VVTFAILEGF RVKAYEKTGE TGLGPFAPFD PLNMRSDETR LKELKNGRLA MLAFLGFSSQ AAVQGKGPIE C LQAHLADP ...String:
RPTWYPGATP PKYLDGTMLG DYGFDPLRLG SKDKDVLKYY REGELTNGRW AMAAVAGILF TDLVGLGPWW EAGAKVESSF DLKTLIIIE VVTFAILEGF RVKAYEKTGE TGLGPFAPFD PLNMRSDETR LKELKNGRLA MLAFLGFSSQ AAVQGKGPIE C LQAHLADP GHNNIFTSSV GNEALAAVLV LSITPCLIEA KNRLQGTDEE EFRPLPW

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #23: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorella ohadii (plant)
Molecular weightTheoretical: 19.911742 KDa
SequenceString:
RTLWLPGIQA PKHLDGKLAG DYGFDPLGLG VDSDRLKWYA EAEKTNGRWA MAAVAGILFT EILGKAKWFE AGAQEYWMDN GPLLAVEAV IMGFLELKRF QGWKETGTSG FLNAFPFDPA GMNSPSMATK EVKNGRLAMT AFVGFAVQAL LTRQGPIEAL Q SHLSSPFT NNFVGSINNL PNVIG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

+
Macromolecule #24: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 24 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 208 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #26: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 26 / Number of copies: 47 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

+
Macromolecule #27: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 27 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #28: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 28 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #29: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 29 / Number of copies: 32 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 24 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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

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

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

+
Macromolecule #32: 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: 32 / Number of copies: 5 / 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 #33: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 33 / Number of copies: 11 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #34: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 34 / Number of copies: 1 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

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

+
Macromolecule #35: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 35 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

+
Macromolecule #36: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 36 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #37: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 37 / Number of copies: 4 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

+
Macromolecule #38: (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: 38 / 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 #39: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 39 / Number of copies: 1 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

+
Macromolecule #40: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 40 / Number of copies: 2 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

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

+
Macromolecule #41: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 41 / Number of copies: 4 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

+
Macromolecule #42: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 42 / Number of copies: 1 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one

+
Macromolecule #43: (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: 43 / Number of copies: 21 / 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 #44: ASTAXANTHIN

MacromoleculeName: ASTAXANTHIN / type: ligand / ID: 44 / Number of copies: 2 / Formula: AXT
Molecular weightTheoretical: 596.838 Da
Chemical component information

ChemComp-AXT:
ASTAXANTHIN

+
Macromolecule #45: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 45 / Number of copies: 4 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

+
Macromolecule #46: (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: 46 / 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 #47: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 47 / Number of copies: 7 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

+
Macromolecule #48: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 48 / Number of copies: 4 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

+
Macromolecule #49: benzene-1,3,5-triol

MacromoleculeName: benzene-1,3,5-triol / type: ligand / ID: 49 / Number of copies: 1 / Formula: 13X
Molecular weightTheoretical: 126.11 Da
Chemical component information

ChemComp-13X:
benzene-1,3,5-triol

+
Macromolecule #50: (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: 50 / Number of copies: 4 / 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 #51: Tripalmitoylglycerol

MacromoleculeName: Tripalmitoylglycerol / type: ligand / ID: 51 / Number of copies: 1 / Formula: 4RF
Molecular weightTheoretical: 807.32 Da
Chemical component information

ChemComp-4RF:
Tripalmitoylglycerol

+
Macromolecule #52: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 52 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

+
Macromolecule #53: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETH...

MacromoleculeName: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
type: ligand / ID: 53 / Number of copies: 1 / Formula: LAP
Molecular weightTheoretical: 440.532 Da
Chemical component information

ChemComp-LAP:
[2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM

+
Macromolecule #54: water

MacromoleculeName: water / type: ligand / ID: 54 / Number of copies: 99 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 4926 / Average exposure time: 1.4 sec. / Average electron dose: 49.05 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 553691
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ijo

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 185138
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: 3 / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ijo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 74.16
Output model

PDB-6zzx:
Structure of low-light grown Chlorella ohadii Photosystem I

+
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