[English] 日本語
Yorodumi
- PDB-6jlu: Structure of PSII-FCP supercomplex from a centric diatom Chaetoce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 ...Peripheral membrane protein) 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 / photosystem II oxygen evolving complex / thylakoid / photosystem II / extrinsic component of membrane / chloroplast thylakoid membrane / photosynthesis, light reaction / phosphate ion binding / photosynthesis ...photosystem II assembly / photosystem II stabilization / photosystem II oxygen evolving complex / thylakoid / photosystem II / extrinsic component of membrane / chloroplast thylakoid membrane / photosynthesis, light reaction / 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 PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...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 PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9839
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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)

-
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

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

#15: Protein Extrinsic protein in photosystem II / Peripheral membrane protein


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 / Peripheral membrane protein


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 / Peripheral membrane protein


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

-
Sugars , 1 types, 14 molecules

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


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

-
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 / Chlorophyll a


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


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


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#36: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


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


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 / Chloride


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


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


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 / 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 / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O3
#45: Chemical...
ChemComp-KC2 / Chlorophyll c2 / Chlorophyll c


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


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

-
Details

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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
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

+
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