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- PDB-6fos: Cyanidioschyzon merolae photosystem I -

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Basic information

Entry
Database: PDB / ID: 6fos
TitleCyanidioschyzon merolae photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 3
  • (Photosystem I iron-sulfur ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • PsaM
  • Similar to chlorophyll a/b-binding protein, CP24
  • Similar to light harvesting protein
KeywordsPHOTOSYNTHESIS / membrane protein / photosynthetic complex / reaction center / photosystem
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / thylakoid / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / thylakoid / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / 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 / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Alpha-Beta Plaits - #20 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / 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. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX ...BETA-CAROTENE / CHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å
AuthorsNelson, N. / Hippler, M. / Antoshvili, M. / Caspy, I.
Funding support Belgium, Israel, 2items
OrganizationGrant numberCountry
European Research Council293579 Belgium
israel science foundation569/17 Israel
CitationJournal: Photosyn. Res. / Year: 2019
Title: Structure and function of photosystem I in Cyanidioschyzon merolae.
Authors: Antoshvili, M. / Caspy, I. / Hippler, M. / Nelson, N.
History
DepositionFeb 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: Similar to chlorophyll a/b-binding protein, CP24
3: Similar to chlorophyll a/b-binding protein, CP24
4: Similar to light harvesting protein
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 p700 chlorophyll A apoprotein A2
E: Photosystem I iron-sulfur center subunit VII
F: Photosystem I reaction center subunit II
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
O: PsaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,733162
Polymers325,75515
Non-polymers125,979147
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37180 Å2
ΔGint-280 kcal/mol
Surface area160290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.130, 213.520, 349.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 4 molecules 234O

#1: Protein Similar to chlorophyll a/b-binding protein, CP24


Mass: 24270.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1UU36
#2: Protein Similar to light harvesting protein


Mass: 23987.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VKK5
#14: Protein PsaM


Mass: 10625.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VFJ4

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Photosystem I P700 chlorophyll a apoprotein ... , 3 types, 3 molecules ABD

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


Mass: 81829.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY7, photosystem I
#4: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 81301.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY6, photosystem I
#6: Protein Photosystem I p700 chlorophyll A apoprotein A2 /


Mass: 13896.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY0

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Photosystem I iron-sulfur ... , 2 types, 2 molecules CE

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


Mass: 8691.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G47, photosystem I
#7: Protein Photosystem I iron-sulfur center subunit VII /


Mass: 7890.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FZ1

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Photosystem I reaction center subunit ... , 6 types, 6 molecules FIJKLM

#8: Protein Photosystem I reaction center subunit II /


Mass: 18055.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FS9
#9: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 3408.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FQ6
#10: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FS8
#11: Protein/peptide Photosystem I reaction center subunit X /


Mass: 4820.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G51
#12: Protein Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 15157.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FP8
#13: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G73

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Non-polymers , 4 types, 147 molecules

#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 134 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#16: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#17: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 80mM MgCl2 , 50mM Citric acid, 4-7.5% PEG 4000, 0.025% alpha-DM, pH 4.8-5.0 or 80mM MgCl2 , 50mM Cacodylate, 4-7.5% PEG 4000, 0.025% alpha-DM, pH 5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 4→49 Å / Num. obs: 41951 / % possible obs: 80.89 % / Redundancy: 12 % / Rpim(I) all: 0.036 / Net I/σ(I): 4
Reflection shellResolution: 4→4.99 Å / Rpim(I) all: 1.236

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Processing

Software
NameVersionClassification
PHENIX(dev_3042: ???)refinement
Aimlessdata scaling
MOLREPphasing
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 4→48.53 Å / SU ML: 0.93 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 55.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4303 842 2.01 %
Rwork0.378 --
obs0.379 41925 80.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21093 0 4518 0 25611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527219
X-RAY DIFFRACTIONf_angle_d1.82938593
X-RAY DIFFRACTIONf_dihedral_angle_d15.08614575
X-RAY DIFFRACTIONf_chiral_restr0.0413358
X-RAY DIFFRACTIONf_plane_restr0.0084720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.25050.5679520.41632793X-RAY DIFFRACTION33
4.2505-4.57840.4347830.35284717X-RAY DIFFRACTION56
4.5784-5.03880.37241560.33597993X-RAY DIFFRACTION95
5.0388-5.76690.38241780.36868425X-RAY DIFFRACTION100
5.7669-7.26170.48431810.44528475X-RAY DIFFRACTION100
7.2617-48.53390.43561920.37048680X-RAY DIFFRACTION100

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