[English] 日本語
Yorodumi
- EMDB-9107: A unique supramolecular organization of photosystem I in the moss... -

+
Open data


ID or keywords:

Loading...

no data

-
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

-
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

-
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

-
Supplemental data

-
Sample components

+
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

+
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

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #11: protein, PsaA

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

+
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)

+
Component #13: protein, PsaB

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

+
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)

+
Component #15: protein, PsaC

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

+
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)

+
Component #17: protein, PsaD

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

+
Component #18: protein, PsaE

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

+
Component #19: protein, PsaF

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

+
Component #20: protein, PsaG

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

+
Component #21: protein, PsaH

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

+
Component #22: protein, PsaI

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

+
Component #23: protein, PsaJ

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

+
Component #24: protein, PsaK

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

+
Component #25: protein, PsaL

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

-
Experimental details

-
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..

-
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)

-
Image acquisition

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

-
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

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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