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- EMDB-7907: Two retinoschisin molecules interacting laterally forming a unit ... -

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Basic information

Entry
Database: EMDB / ID: 7907
TitleTwo retinoschisin molecules interacting laterally forming a unit cell of a filamentous strand.
Map dataRS1 linear strand unit cell with two double octamer ring molecules.
SampleRetinoschisin:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 10 Å resolution
AuthorsHeymann JB / Vijayasarathy C / Huang RK / Dearborn AD / Sieving PA / Steven AC
CitationJournal: J. Cell Biol. / Year: 2019
Title: Cryo-EM of retinoschisin branched networks suggests an intercellular adhesive scaffold in the retina.
Authors: J Bernard Heymann / Camasamudram Vijayasarathy / Rick K Huang / Altaira D Dearborn / Paul A Sieving / Alasdair C Steven
Abstract: Mutations in the retinal protein retinoschisin (RS1) cause progressive loss of vision in young males, a form of macular degeneration called X-linked retinoschisis (XLRS). We previously solved the ...Mutations in the retinal protein retinoschisin (RS1) cause progressive loss of vision in young males, a form of macular degeneration called X-linked retinoschisis (XLRS). We previously solved the structure of RS1, a 16-mer composed of paired back-to-back octameric rings. Here, we show by cryo-electron microscopy that RS1 16-mers can assemble into extensive branched networks. We classified the different configurations, finding four types of interaction between the RS1 molecules. The predominant configuration is a linear strand with a wavy appearance. Three less frequent types constitute the branch points of the network. In all cases, the "spikes" around the periphery of the double rings are involved in these interactions. In the linear strand, a loop (usually referred to as spike 1) occurs on both sides of the interface between neighboring molecules. Mutations in this loop suppress secretion, indicating the possibility of intracellular higher-order assembly. These observations suggest that branched networks of RS1 may play a stabilizing role in maintaining the integrity of the retina.
DateDeposition: May 23, 2018 / Header (metadata) release: Jun 6, 2018 / Map release: Jan 9, 2019 / Last update: Jan 9, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7907.map.gz (map file in CCP4 format, 44958 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
224 pix
1.04 Å/pix.
= 232.96 Å
224 pix
1.04 Å/pix.
= 232.96 Å
224 pix
1.04 Å/pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-4.605874 - 8.537545
Average (Standard dev.)0.000000000012349 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions224224224
Origin-112.0-112.0-112.0
Limit111.0111.0111.0
Spacing224224224
CellA=B=C: 232.95999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z232.960232.960232.960
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-4.6068.5380.000

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Supplemental data

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Mask #1

Fileemd_7907_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Retinoschisin

EntireName: Retinoschisin
Details: Human retinoschisin with a honeybee mellitin leader sequence and a C-terminal 6-histidine tag
Number of components: 2

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Component #1: protein, Retinoschisin

ProteinName: Retinoschisin
Details: Human retinoschisin with a honeybee mellitin leader sequence and a C-terminal 6-histidine tag
Recombinant expression: No
MassTheoretical: 380 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: unidentified baculovirus / Cell of expression system: Sf9

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Component #2: protein, Retinoschisin

ProteinName: Retinoschisin
Details: Mature human RS1 with a C-terminal hexahistidine tag
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: unidentified baculovirus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.4
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 90 %

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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: 0.66 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1136 / Details: 30 degree tilted specimen

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 18646
3D reconstructionAlgorithm: FOURIER SPACE / Software: Bsoft / Resolution: 1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Reconstructed to 3 angstrom, low-pass filtered to 10 angstrom. Symmetrized two-fold (z-axis) and along screw-axis (x-axis).
FSC plot
(resolution estimation)

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