[English] 日本語
Yorodumi
- PDB-5n6w: Retinoschisin R141H Mutant -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5n6w
TitleRetinoschisin R141H Mutant
DescriptorRetinoschisin
KeywordsSTRUCTURAL PROTEIN / Retinoschisin Discoidin Domain Retinal Structure / structural protein
Specimen sourceHomo sapiens / human
MethodElectron microscopy (4.2 Å resolution / Particle / Single particle)
AuthorsRamsay, E.P. / Collins, R.F. / Owens, T.W. / Siebert, C.A. / Jones, R.P.O. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Feb 16, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collection / Experimental preparation / Refinement descriptionem_3d_fitting / em_sample_support / em_software_em_3d_fitting.target_criteria / _em_sample_support.grid_type / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


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

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

Downloads & links

-
Assembly

Deposited unit
A: Retinoschisin
B: Retinoschisin
C: Retinoschisin
D: Retinoschisin
E: Retinoschisin
F: Retinoschisin
G: Retinoschisin
H: Retinoschisin
I: Retinoschisin
J: Retinoschisin
K: Retinoschisin
L: Retinoschisin
M: Retinoschisin
N: Retinoschisin
O: Retinoschisin
P: Retinoschisin


Theoretical massNumber of molelcules
Total (without water)368,67016
Polyers368,67016
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)29630
ΔGint (kcal/M)-130
Surface area (Å2)131310
MethodPISA

-
Components

#1: Polypeptide(L)
Retinoschisin / X-linked juvenile retinoschisis protein


Mass: 23041.902 Da / Num. of mol.: 16 / Mutation: R141H Pathogenic Mutation / Source: (gene. exp.) Homo sapiens / human / References: UniProt: O15537

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: Retinoschisin / Type: COMPLEX
Details: Hexadecameric complex of sixteen retinoschisin molecules
Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Cell: HEK293-EBNA / Organism: Homo sapiens / Plasmid: pCEP-Pu/Ac7
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
110mMTrisC4H11NO31
2150mMSodium ChlorideNaCl1
SpecimenConc.: 0.1 mg/ml / Details: The sample was monodisperse and visible / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 2.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1200
Image scansMovie frames/image: 14 / Used frames/image: 2-8

-
Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1EMAN2.0PARTICLE SELECTION1
4CTFFIND4CTF CORRECTION1
7DockEM2MODEL FITTING1
9EMAN2.0INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
13Flex-EMMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D8
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7056 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

+
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