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- EMDB-6425: Retinoschisin, back-to-back octameric rings -

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Basic information

Entry
Database: EMDB / ID: EMD-6425
TitleRetinoschisin, back-to-back octameric rings
Map dataRetinoschisin double octamer rings
Sample
  • Sample: Mature retinoschisin with a C-terminal hexahistidine tag
  • Protein or peptide: Retinoschisin 1
KeywordsX-linked retinoschisis / discoidin domain / retina / macular degeneration / vision
Function / homology
Function and homology information


neuron to neuron synapse / retina layer formation / : / eye development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylserine binding / visual perception / photoreceptor inner segment / protein homooligomerization / cell adhesion ...neuron to neuron synapse / retina layer formation / : / eye development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylserine binding / visual perception / photoreceptor inner segment / protein homooligomerization / cell adhesion / external side of plasma membrane / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHeymann JB / Tolun G / Vijayasarathy C / Huang R / Zeng Y / Li Y / Steven AC / Sieving PA
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
DepositionAug 12, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseApr 27, 2016-
UpdateJun 8, 2016-
Current statusJun 8, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jd6
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6425.png

Downloads & links

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Map

FileDownload / File: emd_6425.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRetinoschisin double octamer rings
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-3.07950211 - 6.21566534
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 164.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z164.800164.800164.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-3.0806.216-0.000

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Supplemental data

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Sample components

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Entire : Mature retinoschisin with a C-terminal hexahistidine tag

EntireName: Mature retinoschisin with a C-terminal hexahistidine tag
Components
  • Sample: Mature retinoschisin with a C-terminal hexahistidine tag
  • Protein or peptide: Retinoschisin 1

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Supramolecule #1000: Mature retinoschisin with a C-terminal hexahistidine tag

SupramoleculeName: Mature retinoschisin with a C-terminal hexahistidine tag
type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 1
Molecular weightExperimental: 400 KDa / Theoretical: 382 KDa / Method: Blue native gel electrophoresis

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Macromolecule #1: Retinoschisin 1

MacromoleculeName: Retinoschisin 1 / type: protein_or_peptide / ID: 1 / Name.synonym: RS1
Details: The mature RS1 protein (no signal sequence) with a C-terminal six-histidine tag
Number of copies: 16 / Oligomeric state: 16-mer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Retina / Cell: Photoreceptors and bipolar cells / Organelle: Extracellular space / Location in cell: Forming a junction between cells
Molecular weightTheoretical: 24 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pDonr253
SequenceUniProtKB: Retinoschisin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl
GridDetails: C-flat holey carbon grids (2.0 um holes, 2.0 um spaces)
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP / Details: Plunged at room temperature. / Method: Blotted from the copper side.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 39000
Sample stageSpecimen holder model: OTHER
DateJun 11, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 19 / Average electron dose: 30 e/Å2
Details: Each image is the average of 10 frames taken over 3 seconds.
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: Relion, EMAN2, Bsoft / Number images used: 9096
DetailsParticles were picked semi-automatically (EMAN2).
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1sdd

SoftwareName: COOT, MDFF, Foldit
DetailsFlexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: FSC(0.5) = 4.7
Output model

PDB-3jd6:
Double octamer structure of retinoschisin, a cell-cell adhesion protein of the retina

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