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- EMDB-50063: Structure of Far-Red Photosystem I from C. thermalis PCC 7203 -

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Basic information

Entry
Database: EMDB / ID: EMD-50063
TitleStructure of Far-Red Photosystem I from C. thermalis PCC 7203
Map data
Sample
  • Complex: Far Red Photosystem I
    • Protein or peptide: x 12 types
  • Ligand: x 12 types
KeywordsChlorophyll f / Photosystem I / Far-red / cyanobacteria / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / 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 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 reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / 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 XII / Photosystem one PsaX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit IX ...Photosystem I reaction center subunit XII / Photosystem one PsaX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II
Similarity search - Component
Biological speciesC. thermalis (bacteria) / Chroococcidiopsis thermalis PCC 7203 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsConsoli G / Tufaill F / Murray JW / Fantuzzi A / Rutherford AW
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Citation
Journal: To Be Published
Title: Structure of Far-Red Photosystem I from C. thermalis PCC 7203
Authors: Consoli G / Tufail F / Leong H / Fantuzzi A / Rutherford AW
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Murray JW / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / ...Authors: Murray JW / Afonine PV / Baker ML / Bunkoczi G / Chen VB / Croll TI / Hintze B / Hung LW / Jain S / McCoy AJ / Moriarty NW / Oeffner RD / Poon BK / Prisant MG / Read RJ / Richardson JS / Richardson DC / Sammito MD / Sobolev OV / Stockwell DH / Terwilliger TC / Urzhumtsev AG / Videau LL / Williams CJ / Adams PD
History
DepositionApr 9, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50063.png

Downloads & links

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Map

FileDownload / File: emd_50063.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 600 pix.
= 552.6 Å		0.92 Å/pix.
x 600 pix.
= 552.6 Å		0.92 Å/pix.
x 600 pix.
= 552.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054
Minimum - Maximum-0.1624204 - 0.50372154
Average (Standard dev.)0.00010364095 (±0.0092112655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 552.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50063_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50063_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Far Red Photosystem I

EntireName: Far Red Photosystem I
Components
  • Complex: Far Red 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 II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • 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
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem one PsaX
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: Chlorophyll F
  • 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: EICOSANE
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Far Red Photosystem I

SupramoleculeName: Far Red Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Details: Trimeric photosystem I from C. thermalis grown under far-red light condition.
Source (natural)Organism: C. thermalis (bacteria) / Strain: PCC 7203 / Location in cell: thylakoid membrane

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 86.382375 KDa
SequenceString: MTITPEREQK VRVVVDNDPV PTSPELWAKP GHFDRTLARG PKTTTWIWNL HANAHDFDTH TSDLEDISRK IFAAHFGHLA VIFIWLSGM YFHGAKFSNF EAWMANPTGV KPSAQVVWSL VGQDILNADV GGGFHGIQIT SGLFQLWRAA GITNTFQLYC T AIGGLVMA ...String:
MTITPEREQK VRVVVDNDPV PTSPELWAKP GHFDRTLARG PKTTTWIWNL HANAHDFDTH TSDLEDISRK IFAAHFGHLA VIFIWLSGM YFHGAKFSNF EAWMANPTGV KPSAQVVWSL VGQDILNADV GGGFHGIQIT SGLFQLWRAA GITNTFQLYC T AIGGLVMA AIMLFAGWFH YHKRAPKLEW FQNWEAMMNH HLAGLLGLGC LGWAGHQIHV ALPVNKLLDA GVAIKDIPLP HE FILNTSL MAELYPSFAK GLVPFFTLQW GQYADFLTFK GGLNPVTGGL WLSDTAHHHL ALAVLFIVAG HFYRTNWGIG HSF KEMLDD AKSPNMLPFL NFIGPVGHEG LDKIFETSWH ANLSIHLVQF GTASLLVAHH MYAMPPYPYL ATDYATALSL FTHH VWIAG FCIVGGAAHA AIFMVRDYDP AHHVNNILDR TLRHRDVIIS HLAWVCQFLG FHSFAMYCHN DTMRAFGRPQ DMFSD TGIQ LQPIFAQWIQ HIHTAAVGAA QVAQPLGDVF GGVRGIELSG LGTTAPGIGA PVSYAWGGGM VAVGGKVAMM PIALGT ADF LIHHIHAFTI HVTVLVLFKG VLFARGSRLV PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SMVVFHF SW KMQSDVWGTV DSDGIVTHLT GGNFATSSIT NNGWLRDFLW AQSAQVIQSY NSSLSAYGLM FLAGHFIFGF SLMFLFSG R GYWQELIESI VWAHNKLKVA PAIQPRALSI VHGRAVGVAH YLLGGIVTTW AFFLARMSAI G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 83.304703 KDa
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYAMATAHD FELHDGMTEE NLYQKIFASH FGHLAIIFLW ASGVLFHVAW QGNFEQWIKD PLNVRPIAH AIWDAQFGPP AIEAFTRAGA TNPVDICYSG VYHWWYTIGM RTNNELYVGA IFLLLLAALF LFAGWLHLQP R YRPTLGWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYAMATAHD FELHDGMTEE NLYQKIFASH FGHLAIIFLW ASGVLFHVAW QGNFEQWIKD PLNVRPIAH AIWDAQFGPP AIEAFTRAGA TNPVDICYSG VYHWWYTIGM RTNNELYVGA IFLLLLAALF LFAGWLHLQP R YRPTLGWF KSAEPRLNHH LAGLFGVSSL AWAAHLIHVA IPESRGQHVG WDNFLFTPPH PAGLGAFFTG NWSAYAQNPD TA QHVFNSS QGAGTAILTF LGGFHPQTQS LWLTDMAHHH VAIAVLFIIA GHMYRTNWGI GHSIKEMLNS KSFFGAKVEG PFN LPHQGL YDTINNSLHF QLSFALAALG VASSLTAQHM YSMPPYAFIG QDFTTQAALY THHQYIAGFL MVGAFSHAGI FWIR DYDPE QNKGNVLDRM LRHKEAIISH LSWVSLFLGF HTLGLYVHND VEVAFGAAEK QVLIEPVFAQ FIQAAHGKAL YGFNT LLSN PDSIASTAWP NHANVWLPGW LDAVNNTTNS LFLTIGPGDF YVHHAIALGL HVTTLVLVKG ALDARGSKLM PDKKDF GYA FPCDGPGRGG TCDISAWDAS YLAVFWMLNT LGWVTFYWHW KHLAIWEGNI AQFNESSTYL MGWFRDYLWL HSAQLIN GY NPYGTNSLAI WSWMFLWGHL AWAVSFMFLI TWRGYWQELI ETLVWAHEKT PLSFGYWRDK PVALSIVQAR LVGLTHFT V GYIATYGAFL IASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 8.839232 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAAQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 15.798022 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MAETLEGQTP IFGGGTGGLL TKAEREEKYV ITWTSPKEQV FEMPTGGSAI MRQGKNKLEI ARKEYGIALG GQQLRAKFKI NDYKIYRVY PNGETQMIHP ADGVFPEKVN QGRPKVRYVD RNIGSNPSPA KLKFSGVQPY DAP

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 7.634748 KDa
SequenceString:
MVERGSKVRI LRRESYWYQD VGLVASVDKS GIKYPVIVRF DKVNYAGVNT NNFADFELLE IEKPKA

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 17.859723 KDa
SequenceString:
MRRLLFTLAI AFVIWGSTIP TASAANSTLV PCSKSPAFQA RMKNAPDTYY FNKPFKAYAK YELCGTDGLP HLPLDRLDRA TDVLVPIGL FLYVAGFIGW SGRSYLRATK SASDPEMKEI FIDLPLALQS ISKAVLWPLL ALQEFLSGDL TARDEEIPIS P R

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 5.879917 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MVDMTQLTGS YAASWLPWIM IPLIFYILPF PVFALIFIWI EKEAGTADEE V

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 5.297427 KDa
SequenceString:
MQHVFKYLTL APVMATFTMV ALSVVLIMLQ IWFPGLQYGT YFKPTP

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 8.201732 KDa
SequenceString:
MTVPNTISWS PQVALIISAS SLLILLIASR SIKYPQVGAK LPVNLPVLGS PSVGTFVASM AFGHVVGAGI VLGLSNLGWL

UniProtKB: Photosystem I reaction center subunit PsaK

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 19.726336 KDa
SequenceString:
MTNTANPSVE SKLNYRLDTD PVQPYKGDPF NSNFSTAITD SPLARAFINN LPAYRKGLTP FMRGLEIGMA HGYFLVGPEV VVGPLRETA HGANLSGLIT AIYIAVSACL GISIFAITTF QGDPRGAYGS TSKDSLRPLR NRDEWYQLNG GIFLGAMGGA V FAYLLLEN FDALDSILRG GVNVN

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 3.540284 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MMNISDTQVF VALVVALLPG LLAFRLATEL YK

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: Photosystem one PsaX

MacromoleculeName: Photosystem one PsaX / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 3.199871 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
APFPFRTIVS LILLAGNILV AAIYFHIIN

UniProtKB: Photosystem one PsaX

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Macromolecule #13: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 13 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #14: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 14 / Number of copies: 24 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
Chlorophyll F

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Macromolecule #15: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 15 / Number of copies: 246 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #16: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 16 / Number of copies: 6 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #17: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 17 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 66 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 19 / Number of copies: 15 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #20: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 20 / Number of copies: 9 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #21: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 21 / Number of copies: 15 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #22: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 22 / Number of copies: 6 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

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Macromolecule #23: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 23 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #24: water

MacromoleculeName: water / type: ligand / ID: 24 / Number of copies: 405 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 6.5
Details: 20 mM MES NaOH pH 6.5 5 mM CaCl2 5 mM MgCl2 0.03% betaDM
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was monodisperse, but the concentration high

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8854 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1560000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83138
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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  • 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

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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

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