[English] 日本語
Yorodumi
- EMDB-3825: Three-dimensional cryo-EM density map of paired C2S2M PSII-LHCII ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3825
TitleThree-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Samplepaired PSII-LHCII supercomplexes from pea plants
SourcePisum sativum / plant / peas / エンドウ
Map dataThree-dimensional cryo-EM density map of paired C2S2M PSII-LHCII supercomplexes from thylakoid membranes of Pisum sativum
Methodsingle particle reconstruction, at 14 Å resolution
AuthorsPagliano C
CitationSci Rep, 2017, 7, 10067-10067

Sci Rep, 2017, 7, 10067-10067 StrPapers
Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap.
Pascal Albanese / Roberto Melero / Benjamin D Engel / Alessandro Grinzato / Paola Berto / Marcello Manfredi / Angelica Chiodoni / Javier Vargas / Carlos Óscar Sánchez Sorzano / Emilio Marengo / Guido Saracco / Giuseppe Zanotti / Jose-Maria Carazo / Cristina Pagliano

DateDeposition: Jul 26, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Sep 6, 2017 / Last update: Sep 20, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0003
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_3825.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.4 Å/pix.
= 560. Å
400 pix
1.4 Å/pix.
= 560. Å
400 pix
1.4 Å/pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.0003 (by author), 0.0003 (movie #1):
Minimum - Maximum-0.0027011025 - 0.022493664
Average (Standard dev.)8.22539E-5 (0.00074280193)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin000
Limit399399399
Spacing400400400
CellA=B=C: 560 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0030.0220.000

-
Supplemental data

-
Sample components

-
Entire paired PSII-LHCII supercomplexes from pea plants

EntireName: paired PSII-LHCII supercomplexes from pea plants
Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Number of components: 1
MassTheoretical: 2.75 MDa

-
Component #1: protein, paired PSII-LHCII supercomplexes from pea plants

ProteinName: paired PSII-LHCII supercomplexes from pea plants
Details: paired PSII-LHCII supercomplexes connected across the stromal gap
Recombinant expression: No
MassTheoretical: 2.75 MDa
SourceSpecies: Pisum sativum / plant / peas / エンドウ / Strain: Palladio nano
Source (natural)Organelle: Chloroplast / Organ or tissue: Mesophyll

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: fresh solution / pH: 5.7
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 294 K / Humidity: 100 % / Details: blot for 4 seconds befoere plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 6834

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 26953
3D reconstructionSoftware: SCIPION / Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

+
About Yorodumi

-
News

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more