[English] 日本語
Yorodumi
- PDB-3jd6: Double octamer structure of retinoschisin, a cell-cell adhesion p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jd6
TitleDouble octamer structure of retinoschisin, a cell-cell adhesion protein of the retina
ComponentsRetinoschisin
KeywordsCELL ADHESION / discoidin domain / double octamer / adhesion protein / X-linked retinoschisis
Function / homology
Function and homology information


neuron to neuron synapse / retina layer formation / eye development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylserine binding / photoreceptor inner segment / visual perception / protein homooligomerization / cell adhesion / external side of plasma membrane ...neuron to neuron synapse / retina layer formation / eye development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylserine binding / photoreceptor inner segment / visual perception / protein homooligomerization / cell adhesion / external side of plasma membrane / protein-containing complex binding / protein-containing complex / extracellular space
Similarity search - Function
Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsTolun, G. / Vijayasarathy, C. / Huang, R. / Zeng, Y. / Li, Y. / Steven, A.C. / Sieving, P.A. / Heymann, J.B.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Paired octamer rings of retinoschisin suggest a junctional model for cell-cell adhesion in the retina.
Authors: Gökhan Tolun / Camasamudram Vijayasarathy / Rick Huang / Yong Zeng / Yan Li / Alasdair C Steven / Paul A Sieving / J Bernard Heymann /
Abstract: Retinoschisin (RS1) is involved in cell-cell junctions in the retina, but is unique among known cell-adhesion proteins in that it is a soluble secreted protein. Loss-of-function mutations in RS1 lead ...Retinoschisin (RS1) is involved in cell-cell junctions in the retina, but is unique among known cell-adhesion proteins in that it is a soluble secreted protein. Loss-of-function mutations in RS1 lead to early vision impairment in young males, called X-linked retinoschisis. The disease is characterized by separation of inner retinal layers and disruption of synaptic signaling. Using cryo-electron microscopy, we report the structure at 4.1 Å, revealing double octamer rings not observed before. Each subunit is composed of a discoidin domain and a small N-terminal (RS1) domain. The RS1 domains occupy the centers of the rings, but are not required for ring formation and are less clearly defined, suggesting mobility. We determined the structure of the discoidin rings, consistent with known intramolecular and intermolecular disulfides. The interfaces internal to and between rings feature residues implicated in X-linked retinoschisis, indicating the importance of correct assembly. Based on this structure, we propose that RS1 couples neighboring membranes together through octamer-octamer contacts, perhaps modulated by interactions with other membrane components.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

-
Structure visualization

Movie
  • Biological unit as complete point assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6425
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: Retinoschisin


Theoretical massNumber of molelcules
Total (without water)23,8901
Polymers23,8901
Non-polymers00
Water00
1
O: Retinoschisin
x 16


Theoretical massNumber of molelcules
Total (without water)382,23716
Polymers382,23716
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation16
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D8 (2x8 fold dihedral))

-
Components

#1: Protein Retinoschisin / RS1 / X-linked juvenile retinoschisis protein


Mass: 23889.830 Da / Num. of mol.: 1 / Fragment: UNP residues 24-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RS1, XLRS1 / Plasmid: 11109-E01 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O15537

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Purified Retinoschisin: residues 24-224 + 6xHis / Type: COMPLEX / Synonym: RS1
Buffer solutionName: 20 mM Tris-HCl, 150 mM NaCl / pH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Plasma-cleaned 2.0 um hole, 2.0 um space C-flat holey carbon grids (Protochips)
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 %
Details: Ambient temperature 23 degrees C. Plunged into liquid ethane (LEICA EM GP).

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jun 3, 2014 / Details: 10 frames over 3 seconds
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: FEI Polara specimen loader
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) / Details: Counting mode
Image scansNum. digital images: 19

-
Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2Folditmodel fitting
3MDFFmodel fitting
4EMAN23D reconstruction
5RELION3D reconstruction
CTF correctionDetails: Included in iterative refinement
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionMethod: Bayesian orientation refinement with iterative gridded reconstruction
Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9096 / Nominal pixel size: 1.03 Å / Actual pixel size: 1.03 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: FSC(0.5) = 4.7
Details: METHOD--Flexible fitting REFINEMENT PROTOCOL--FLEXIBLE
Atomic model buildingPDB-ID: 1SDD

1sdd

Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 0 0 1367

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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