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- PDB-9jj8: Structural insights into the PSI-FCPI supercomplex from the cocco... -

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Basic information

Entry
Database: PDB / ID: 9jj8
TitleStructural insights into the PSI-FCPI supercomplex from the coccolithophore Emiliania huxleyi
Components
  • (Light harvesting ...) x 25
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 7
  • Linker-protein
  • PSI-K
  • Photosystem I iron-sulfur center
  • PsaR
KeywordsPHOTOSYNTHESIS / PSI-FCPI supercomplex
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
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 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 / 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 / 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
: / : / : / Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...: / : / : / Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / PSI-K / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Uncharacterized protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Light harvesting protein / Photosystem I reaction center subunit IV / Light harvesting protein / Light harvesting protein
Similarity search - Component
Biological speciesEmiliania huxleyi CCMP1516 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsShen, L.L. / Li, Z.H. / Wang, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural insights into the PSI-FCPI supercomplex from the coccolithophore Emiliania huxleyi
Authors: Shen, L.L. / Li, Z.H. / Wang, W.D.
History
DepositionSep 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
k: PSI-K
o: Linker-protein
A: Light harvesting protein
B: Light harvesting protein
C: Light harvesting protein
D: Light harvesting protein
E: Light harvesting protein
F: Light harvesting protein
G: Light harvesting protein
H: Light harvesting protein
J: Light harvesting protein
K: Light harvesting protein
L: Light harvesting protein
M: Light harvesting protein
O: Light harvesting protein
P: Light harvesting protein
Q: Light harvesting protein
R: Light harvesting protein
S: Light harvesting protein
T: Light harvesting protein
U: Light harvesting protein
V: Light harvesting protein
W: Light harvesting protein
X: Light harvesting protein
0: Light harvesting protein
1: Light harvesting protein
3: Light harvesting protein
4: Light harvesting protein
5: Light harvesting protein
7: Light harvesting protein
8: Light harvesting protein
9: Light harvesting protein
I: Light harvesting protein
h: PsaR
x: Light harvesting protein
y: Light harvesting protein
z: Light harvesting protein
Y: Light harvesting protein
Z: Light harvesting protein
2: Light harvesting protein
6: Light harvesting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,907,799920
Polymers1,237,46251
Non-polymers670,337869
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules ab

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 83647.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3F6, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82100.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3F5, photosystem I

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Protein , 4 types, 4 molecules ckoh

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3C1, photosystem I
#11: Protein PSI-K / Photosystem I subunit X


Mass: 15001.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A7S3X4W4
#12: Protein Linker-protein


Mass: 12203.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DLA7
#37: Protein PsaR


Mass: 13621.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote)

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Photosystem I reaction center subunit ... , 7 types, 7 molecules defijlm

#4: Protein Photosystem I reaction center subunit II / PsaD


Mass: 15898.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G369
#5: Protein Photosystem I reaction center subunit IV / PsaE


Mass: 13523.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1EZZ6
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20000.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3B9
#7: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3971.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G373
#8: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4539.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3B8
#9: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15488.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G3B5
#10: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3213.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: Q4G371

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Light harvesting ... , 25 types, 38 molecules ABCDEFGHJKLMPWOQRVX5S47xyzTU01...

#13: Protein Light harvesting protein / FCPI-7


Mass: 21992.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1FED1
#14: Protein Light harvesting protein / FCPI-1


Mass: 18812.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1D5F1
#15: Protein Light harvesting protein / FCPI-11


Mass: 24673.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A6V2SE28
#16: Protein Light harvesting protein / FCPI-6


Mass: 24534.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1ESZ0
#17: Protein Light harvesting protein / FCPI-5


Mass: 22394.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DEA6
#18: Protein Light harvesting protein / FCPI-8


Mass: 25430.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DWS2
#19: Protein Light harvesting protein / FCPI-4


Mass: 22109.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1B3D6
#20: Protein Light harvesting protein / FCPI-10


Mass: 22349.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A7S3WIW7
#21: Protein Light harvesting protein / FCPI-9


Mass: 26404.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A7S3TG01
#22: Protein Light harvesting protein / FCPI-15


Mass: 20760.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DY94
#23: Protein Light harvesting protein / FCPI-18


Mass: 26276.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1FP66
#24: Protein Light harvesting protein / FCPI-23/20/27


Mass: 23617.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1BTM8
#25: Protein Light harvesting protein / FCPI-12


Mass: 22875.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A7S3WZA0
#26: Protein Light harvesting protein / FCPI-21


Mass: 27669.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1EB65
#27: Protein
Light harvesting protein


Mass: 22601.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote)
#28: Protein
Light harvesting protein / R1EIA6


Mass: 27307.240 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1EIA6
#29: Protein Light harvesting protein / FCPI-13


Mass: 22478.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DMQ2
#30: Protein Light harvesting protein / FCPI-2


Mass: 21708.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1ED82
#31: Protein Light harvesting protein / FCPI-16


Mass: 27517.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1CV07
#32: Protein Light harvesting protein / FCPI-22


Mass: 27282.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1CMT6
#33: Protein Light harvesting protein


Mass: 28328.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DAV6
#34: Protein Light harvesting protein


Mass: 26786.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote)
#35: Protein Light harvesting protein


Mass: 26548.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1DNR0
#36: Protein Light harvesting protein


Mass: 22288.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: A0A7S3TFW5
#38: Protein Light harvesting protein


Mass: 28110.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Emiliania huxleyi CCMP1516 (eukaryote) / References: UniProt: R1CGG7

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Sugars , 1 types, 2 molecules

#45: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 13 types, 867 molecules

#39: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 411 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#41: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#42: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#44: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#46: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#47: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#48: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 100 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical...
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 113 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical...
ChemComp-A1EB1 / [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-2-[2-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]ethenyl]-6,11,15-trimethyl-16-oxidanylidene-17-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]heptadeca-2,4,6,8,10,12,14-heptaenyl] hexanoate / 19'-Hexanoyloxyfucoxanthin


Mass: 773.049 Da / Num. of mol.: 67 / Source method: obtained synthetically / Formula: C48H68O8 / Feature type: SUBJECT OF INVESTIGATION
#51: Chemical...
ChemComp-A1ECV / Chlorophyll C3 / magnesium;(E)-3-[(3R)-11,16-bis(ethenyl)-3,12-bis(methoxycarbonyl)-17,21,26-trimethyl-4-oxido-7,23,24,25-tetrazahexacyclo[18.2.1.15,8.110,13.115,18.02,6]hexacosa-1,4,6,8(26),9,11,13,15(24),16,18,20(23),21-dodecaen-22-yl]prop-2-enoate


Mass: 652.935 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C36H28MgN4O7 / Feature type: SUBJECT OF INVESTIGATION
#52: Chemical
ChemComp-A1EB4 / [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[2-[(1~{R},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethynyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] dodecanoate / Gallate


Mass: 839.193 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C54H78O7 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Eh-PSI-FCPI / Type: COMPLEX / Entity ID: #1-#38 / Source: NATURAL
Source (natural)Organism: Emiliania huxleyi CCMP1516 (eukaryote)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70606 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007121018
ELECTRON MICROSCOPYf_angle_d2.138175104
ELECTRON MICROSCOPYf_dihedral_angle_d21.92923307
ELECTRON MICROSCOPYf_chiral_restr0.06314631
ELECTRON MICROSCOPYf_plane_restr0.00722274

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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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