[English] 日本語
Yorodumi
- EMDB-3595: Retinoschisin R141H Mutant -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3595
TitleRetinoschisin R141H Mutant
SampleRetinoschisin
SourceHomo sapiens / human
Map dataRetinoschisin R141H D8 Hexadecameric Complex
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsRamsay EP / Collins RF / Owens TW / Siebert CA / Jones RPO / Roseman A / Wang T / Baldock C
CitationHum. Mol. Genet., 2016, 25, 5311-5320

Hum. Mol. Genet., 2016, 25, 5311-5320 Yorodumi Papers
Structural analysis of X-linked retinoschisis mutations reveals distinct classes which differentially effect retinoschisin function.
Ewan P Ramsay / Richard F Collins / Thomas W Owens / C Alistair Siebert / Richard P O Jones / Tao Wang / Alan M Roseman / Clair Baldock

Validation ReportPDB-ID: 5n6w

SummaryFull reportAbout validation report
DateDeposition: Feb 16, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: Apr 12, 2017 / Last update: Aug 30, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5n6w
  • Surface level: 0.03
  • 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_3595.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.29 Å/pix.
= 330.24 Å
256 pix
1.29 Å/pix.
= 330.24 Å
256 pix
1.29 Å/pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.29 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.04040661 - 0.07888982
Average (Standard dev.)0.00025765845 (0.0039747357)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 330.24 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z330.240330.240330.240
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0400.0790.000

-
Supplemental data

-
Sample components

-
Entire Retinoschisin

EntireName: Retinoschisin
Details: Hexadecameric complex of sixteen retinoschisin molecules
Number of components: 2

-
Component #1: protein, Retinoschisin

ProteinName: Retinoschisin
Details: Hexadecameric complex of sixteen retinoschisin molecules
Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Vector: pCEP-Pu/Ac7 / Cell of expression system: HEK293-EBNA

-
Component #2: protein, Retinoschisin

ProteinName: Retinoschisin / Recombinant expression: No
MassTheoretical: 23.041902 kDa
Source (engineered)Expression System: Homo sapiens / human / Vector: pCEP-Pu/Ac7

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 2.8 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1200

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D8 (2*8 fold dihedral) / Number of projections: 7056
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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