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- EMDB-9107: A unique supramolecular organization of photosystem I in the moss... -

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Basic information

Entry
Database: EMDB / ID: 9107
TitleA unique supramolecular organization of photosystem I in the moss Physcomitrella patens
Map dataLarge Physcomitrella patens PSI-LHCI supercomplex map from cryo-EM
SampleLarge PSI-LHCI supercomplex
  • (Chlorophyll A/B binding protein ...) x 12
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaKPosek
  • PsaL
SourcePhyscomitrella patens (plant)
Methodsingle particle reconstruction / cryo EM / 11.6 Å resolution
AuthorsIwai M / Grob P
CitationJournal: Nat Plants / Year: 2018
Title: A unique supramolecular organization of photosystem I in the moss Physcomitrella patens.
Authors: Masakazu Iwai / Patricia Grob / Anthony T Iavarone / Eva Nogales / Krishna K Niyogi
Validation ReportPDB-ID: 6mem

SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mem
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9107.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.8 Å/pix.
= 358.4 Å
128 pix
2.8 Å/pix.
= 358.4 Å
128 pix
2.8 Å/pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-0.24073532 - 0.6912893
Average (Standard dev.)0.0022492264 (0.068978965)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.00.00.0
Limit127.0127.0127.0
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2410.6910.002

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Supplemental data

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Sample components

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Entire Large PSI-LHCI supercomplex

EntireName: Large PSI-LHCI supercomplex
Details: A protein supercomplex isolated by gentle detergent solubilization of thylakoid membranes and maltose density gradient centrifugation
Number of components: 25

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Component #1: protein, Large PSI-LHCI supercomplex

ProteinName: Large PSI-LHCI supercomplex
Details: A protein supercomplex isolated by gentle detergent solubilization of thylakoid membranes and maltose density gradient centrifugation
Recombinant expression: No
MassTheoretical: 940 kDa
SourceSpecies: Physcomitrella patens (plant) / Strain: Gransden 2004

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Component #2: protein, Chlorophyll A/B binding protein 1

ProteinName: Chlorophyll A/B binding protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.443229 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #3: protein, Chlorophyll A/B binding protein 5

ProteinName: Chlorophyll A/B binding protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.613436 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #4: protein, Chlorophyll A/B binding protein 3

ProteinName: Chlorophyll A/B binding protein 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.719787 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #5: protein, Chlorophyll A/B binding protein 7

ProteinName: Chlorophyll A/B binding protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.54958 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #6: protein, Chlorophyll A/B binding protein 4

ProteinName: Chlorophyll A/B binding protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.826139 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #7: protein, Chlorophyll A/B binding protein 9

ProteinName: Chlorophyll A/B binding protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.570826 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #8: protein, Chlorophyll A/B binding protein 8

ProteinName: Chlorophyll A/B binding protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.65593 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #9: protein, Chlorophyll A/B binding protein 2

ProteinName: Chlorophyll A/B binding protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.868748 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #10: protein, Chlorophyll A/B binding protein 6

ProteinName: Chlorophyll A/B binding protein 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.698539 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #11: protein, PsaA

ProteinName: PsaA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.250809 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #12: protein, Chlorophyll A/B binding protein 10

ProteinName: Chlorophyll A/B binding protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.996346 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #13: protein, PsaB

ProteinName: PsaB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.399789 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #14: protein, Chlorophyll A/B binding protein 11

ProteinName: Chlorophyll A/B binding protein 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.081451 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #15: protein, PsaC

ProteinName: PsaC / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.826406 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #16: protein, Chlorophyll A/B binding protein 12

ProteinName: Chlorophyll A/B binding protein 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.166555 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #17: protein, PsaD

ProteinName: PsaD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.188016 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #18: protein, PsaE

ProteinName: PsaE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.634938 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #19: protein, PsaF

ProteinName: PsaF / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.12417 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #20: protein, PsaG

ProteinName: PsaG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.273189 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #21: protein, PsaH

ProteinName: PsaH / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.507245 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #22: protein, PsaI

ProteinName: PsaI / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.571161 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #23: protein, PsaJ

ProteinName: PsaJ / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.592419 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #24: protein, PsaK

ProteinName: PsaKPosek / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.571091 kDa
SourceSpecies: Physcomitrella patens (plant)

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Component #25: protein, PsaL

ProteinName: PsaL / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.379484 kDa
SourceSpecies: Physcomitrella patens (plant)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 % / Details: Lights off, blot 4.5 seconds before plunging..

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000.0 X (nominal), 107140.0 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: -2500.0 - -1800.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 93.0 - 93.0 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 361 / Sampling size: 15 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 14412
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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