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- PDB-6jlu: Structure of PSII-FCP supercomplex from a centric diatom Chaetoce... -

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Entry
Database: PDB / ID: 6jlu
TitleStructure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis at 3.02 angstrom resolution
Components
  • (Extrinsic protein in photosystem ...) x 3
  • (Photosystem II reaction center ...) x 2
  • Cytochrome c-550
  • FCP-A
  • FCP-D
  • FCP-E
  • FCP-F
  • Psb31
  • Psb34
  • PsbA
  • PsbB
  • PsbC
  • PsbD
  • PsbE
  • PsbF
  • PsbG
  • PsbI
  • PsbJ
  • PsbK
  • PsbL
  • PsbM
  • PsbT
  • PsbW
  • PsbY
  • PsbZ
KeywordsPLANT PROTEIN / PSII-FCP supercomplex
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / photosynthesis / respiratory electron transport chain ...photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding
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 PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily ...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 PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 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 / Chlorophyll c2 ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / 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: 3.02 Å
AuthorsPi, X. / Zhao, S. / Wang, W. / Kuang, T. / Sui, S. / Shen, J.
CitationJournal: Science / Year: 2019
Title: The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex.
Authors: Xiong Pi / Songhao Zhao / Wenda Wang / Desheng Liu / Caizhe Xu / Guangye Han / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light ...Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II (PSII)-fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.
History
DepositionMar 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: PsbA
B: PsbB
C: PsbC
D: PsbD
E: PsbE
F: PsbF
G: Psb31
H: Photosystem II reaction center protein H
I: PsbI
J: PsbJ
K: PsbK
L: PsbL
M: PsbM
N: Psb34
O: Extrinsic protein in photosystem II
P: FCP-D
Q: Extrinsic protein in photosystem II
R: PsbG
T: PsbT
U: Extrinsic protein in photosystem II
V: Cytochrome c-550
W: PsbW
X: Photosystem II reaction center X protein
Y: PsbY
Z: PsbZ
a: PsbA
b: PsbB
c: PsbC
d: PsbD
e: PsbE
f: PsbF
g: Psb31
h: Photosystem II reaction center protein H
i: PsbI
j: PsbJ
k: PsbK
l: PsbL
m: PsbM
n: Psb34
o: Extrinsic protein in photosystem II
p: FCP-D
q: Extrinsic protein in photosystem II
r: PsbG
t: PsbT
u: Extrinsic protein in photosystem II
v: Cytochrome c-550
w: PsbW
x: Photosystem II reaction center X protein
y: PsbY
z: PsbZ
0: FCP-E
1: FCP-A
2: FCP-A
3: FCP-A
4: FCP-A
5: FCP-A
6: FCP-A
7: FCP-A
8: FCP-A
9: FCP-F
10: FCP-E
11: FCP-A
12: FCP-A
13: FCP-A
14: FCP-A
15: FCP-A
16: FCP-A
17: FCP-A
18: FCP-A
19: FCP-F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,534,413606
Polymers1,124,52570
Non-polymers409,888536
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, PSII-FCP supercomplex
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 14 types, 42 molecules AaBbCcDdEeGgPpRrVvWwZz010123456...

#1: Protein PsbA


Mass: 39575.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#2: Protein PsbB


Mass: 56475.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#3: Protein PsbC


Mass: 49357.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#4: Protein PsbD


Mass: 37983.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#5: Protein PsbE


Mass: 9062.132 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#7: Protein Psb31


Mass: 18733.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#16: Protein FCP-D


Mass: 24667.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#18: Protein PsbG


Mass: 6230.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#21: Protein Cytochrome c-550 / Cytochrome c550


Mass: 14920.837 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF4
#22: Protein PsbW


Mass: 5720.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#25: Protein PsbZ


Mass: 6417.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#26: Protein FCP-E


Mass: 18781.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#27: Protein
FCP-A


Mass: 18988.840 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#28: Protein FCP-F


Mass: 18214.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Protein/peptide , 9 types, 18 molecules FfIiJjKkLlMmNnTtYy

#6: Protein/peptide PsbF


Mass: 3652.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#9: Protein/peptide PsbI


Mass: 3940.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#10: Protein/peptide PsbJ


Mass: 3487.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#11: Protein/peptide PsbK


Mass: 4225.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#12: Protein/peptide PsbL


Mass: 4367.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#13: Protein/peptide PsbM


Mass: 4358.022 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#14: Protein/peptide Psb34


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


Mass: 3711.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#24: Protein/peptide PsbY


Mass: 3634.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Photosystem II reaction center ... , 2 types, 4 molecules HhXx

#8: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7188.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7XBY7
#23: Protein/peptide Photosystem II reaction center X protein


Mass: 3502.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF2

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

#15: Protein Extrinsic protein in photosystem II


Mass: 26820.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE8
#17: Protein Extrinsic protein in photosystem II


Mass: 22585.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHE9
#20: Protein Extrinsic protein in photosystem II


Mass: 10167.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B6ZHF0

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Sugars , 1 types, 14 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 17 types, 523 molecules

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


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


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


Mass: 893.489 Da / Num. of mol.: 230 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#32: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#34: 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
#35: 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
#36: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#37: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#38: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C45H86O10
#40: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#41: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 610.941 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#43: 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.: 124 / Source method: obtained synthetically / Formula: C42H58O6
#44: 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.: 2 / Source method: obtained synthetically / Formula: C40H54O3
#45: Chemical...
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: C35H28MgN4O5
#46: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsComplete sequence of entities Psb34, PsbR, PsbW and FCP-E are unknown.

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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: PSII-FCP supercomplex / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Source (natural)Organism: Chaetoceros gracilis (Diatom)
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: 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: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
12RELION3classification
13RELION33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42033 / Symmetry type: POINT

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