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- PDB-7vd5: Structure of C2S2M2-type PSII-FCPII supercomplex from diatom -

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Basic information

Entry
Database: PDB / ID: 7vd5
TitleStructure of C2S2M2-type PSII-FCPII supercomplex from diatom
Components
  • (Chlorophyll a/b-binding ...) x 5
  • (Cytochrome b559 subunit ...) x 2
  • (Extrinsic protein in photosystem ...) x 3
  • (Photosystem II ...) x 15
  • (Unknown protein ...) x 2
  • Cytochrome c-550
  • Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
KeywordsELECTRON TRANSPORT / Photosystem / PSII
Function / homology
Function and homology information


light-harvesting complex / thylakoid / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / response to herbicide ...light-harvesting complex / thylakoid / photosynthesis, light harvesting / photosystem II assembly / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / chloroplast / respiratory electron transport chain / oxidoreductase activity / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ ...PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Cytochrome b559 subunit beta / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K / Chlorophyll a/b-binding protein / Photosystem II D2 protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Z / Photosystem II protein D1 / Photosystem II reaction center protein L / Photosystem II reaction center protein J / Photosystem II subunit / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II reaction center protein W / Extrinsic protein in photosystem II / Extrinsic protein in photosystem II / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein X / Photosystem II extrinsic protein V / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsNagao, R. / Kato, K. / Akita, F. / Miyazaki, N. / Shen, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Authors: Nagao, R. / Kato, K. / Kumazawa, M. / Ifuku, K. / Yokono, M. / Suzuki, T. / Dohmae, N. / Akita, F. / Akimoto, S. / Miyazaki, N. / Shen, J.R.
History
DepositionSep 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II subunit
O: Extrinsic protein in photosystem II
T: Photosystem II reaction center protein T
U: Extrinsic protein in photosystem II
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
Q: Extrinsic protein in photosystem II
W: Photosystem II reaction center protein W
0: Unknown protein 0
1: Unknown protein 1
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II subunit
o: Extrinsic protein in photosystem II
t: Photosystem II reaction center protein T
u: Extrinsic protein in photosystem II
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
q: Extrinsic protein in photosystem II
w: Photosystem II reaction center protein W
5: Unknown protein 0
6: Unknown protein 1
11: Chlorophyll a/b-binding protein
12: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
13: Chlorophyll a/b-binding protein
14: Chlorophyll a/b-binding protein
15: Chlorophyll a/b-binding protein
16: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
17: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
18: Chlorophyll a/b-binding protein
19: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
20: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
21: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
31: Chlorophyll a/b-binding protein
32: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
33: Chlorophyll a/b-binding protein
34: Chlorophyll a/b-binding protein
35: Chlorophyll a/b-binding protein
36: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
37: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
38: Chlorophyll a/b-binding protein
39: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
40: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
41: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,435,332616
Polymers1,049,64568
Non-polymers385,687548
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 15 types, 30 molecules AaBbCcDdHhIiJjKkLlMmTtYyXxZzWw

#1: Protein Photosystem II protein D1


Mass: 37036.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C261
#2: Protein Photosystem II CP47 reaction center protein


Mass: 53762.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E3
#3: Protein Photosystem II CP43 reaction center protein


Mass: 49468.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVV7
#4: Protein Photosystem II D2 protein


Mass: 37983.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C012
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7287.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7XBY7
#8: Protein/peptide Photosystem II reaction center protein I


Mass: 4069.853 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT8
#9: Protein/peptide Photosystem II reaction center protein J


Mass: 3589.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C298
#10: Protein/peptide Photosystem II reaction center protein K


Mass: 4220.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BWI3
#11: Protein/peptide Photosystem II reaction center protein L


Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C262
#12: Protein/peptide Photosystem II subunit


Mass: 4473.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C2A0
#14: Protein/peptide Photosystem II reaction center protein T


Mass: 3554.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E6
#17: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3609.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT2
#18: Protein/peptide Photosystem II reaction center X protein


Mass: 3772.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF2
#19: Protein Photosystem II reaction center protein Z


Mass: 6328.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C215
#21: Protein Photosystem II reaction center protein W


Mass: 5944.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C6E8

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 8687.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679C209
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3207.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BVT0

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Extrinsic protein in photosystem ... , 3 types, 6 molecules OoUuQq

#13: Protein Extrinsic protein in photosystem II


Mass: 26419.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE8
#15: Protein Extrinsic protein in photosystem II / Extrinsic protein U of oxygen-evolving complex


Mass: 10137.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF0
#20: Protein Extrinsic protein in photosystem II


Mass: 16731.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE9

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Protein , 7 types, 14 molecules Vv123216361737193920402141

#16: Protein Cytochrome c-550 / Cytochrome c550


Mass: 14780.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF4
#25: Protein Fcpb2, Fucoxanthin chlorophyll a/c-binding protein


Mass: 18525.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#29: Protein Fcpb3, Fucoxanthin chlorophyll a/c-binding protein


Mass: 19620.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#30: Protein Fcpb4, Fucoxanthin chlorophyll a/c-binding protein


Mass: 19202.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#32: Protein Fcpb5, Fucoxanthin chlorophyll a/c-binding protein


Mass: 24681.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#33: Protein Fcpb6, Fucoxanthin chlorophyll a/c-binding protein


Mass: 16968.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#34: Protein Fcpb7, Fucoxanthin chlorophyll a/c-binding protein


Mass: 17888.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Unknown protein ... , 2 types, 4 molecules 0516

#22: Protein/peptide Unknown protein 0


Mass: 2656.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#23: Protein/peptide Unknown protein 1


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Chlorophyll a/b-binding ... , 5 types, 10 molecules 11311333143415351838

#24: Protein Chlorophyll a/b-binding protein


Mass: 19109.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6
#26: Protein Chlorophyll a/b-binding protein


Mass: 18448.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6
#27: Protein Chlorophyll a/b-binding protein


Mass: 18768.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6
#28: Protein Chlorophyll a/b-binding protein


Mass: 18596.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6
#31: Protein Chlorophyll a/b-binding protein


Mass: 18351.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6

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Sugars , 2 types, 10 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15
#51: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 16 types, 590 molecules

#35: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#36: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#37: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 220 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#38: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#39: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#40: 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.: 10 / Source method: obtained synthetically / Formula: C41H78O12S
#41: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#42: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#43: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#45: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#46: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#47: Chemical...
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#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.: 108 / Source method: obtained synthetically / Formula: C42H58O6
#49: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 38 / Source method: obtained synthetically
#50: 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.: 12 / Source method: obtained synthetically / Formula: C40H54O3
#52: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY
Sequence detailsAuthors do not know the sequences for chain 0, 1, 5, and 6.

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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: C2S2M2-type PSII-FCPII supercomplex / Type: COMPLEX / Entity ID: #1-#30 / Source: NATURAL
Molecular weightValue: 1.15 MDa / Experimental value: NO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.02 %DDM1
SpecimenConc.: 0.256 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8093924
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210825 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6J40

6j40


Accession code: 6J40 / Source name: PDB / Type: experimental model

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