[English] 日本語
Yorodumi
- EMDB-7907: Two retinoschisin molecules interacting laterally forming a unit ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-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.
Sample
  • Complex: Retinoschisin
    • Protein or peptide: Retinoschisin
KeywordsRetinal adhesion protein X-linked retinoschisis Discoidin domain / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
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.
History
DepositionMay 23, 2018-
Header (metadata) releaseJun 6, 2018-
Map releaseJan 9, 2019-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_7907.png

Downloads & links

-
Map

FileDownload / File: emd_7907.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRS1 linear strand unit cell with two double octamer ring molecules.
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-4.605874 - 8.537545
Average (Standard dev.)0.000000000012349 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 232.95999 Å
α=β=γ: 90.0 °

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-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-4.6068.5380.000

-
Supplemental data

-
Mask #1

Fileemd_7907_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Second half map of RS1 unit

Fileemd_7907_half_map_1.map
AnnotationSecond half map of RS1 unit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: First half map of the RS1 unit cell

Fileemd_7907_half_map_2.map
AnnotationFirst half map of the RS1 unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Retinoschisin

EntireName: Retinoschisin
Components
  • Complex: Retinoschisin
    • Protein or peptide: Retinoschisin

-
Supramolecule #1: Retinoschisin

SupramoleculeName: Retinoschisin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human retinoschisin with a honeybee mellitin leader sequence and a C-terminal 6-histidine tag
Source (natural)Organism: Homo sapiens (human) / Organ: Eye / Tissue: Retina / Location in cell: Intercellular space
Molecular weightTheoretical: 380 KDa

-
Macromolecule #1: Retinoschisin

MacromoleculeName: Retinoschisin / type: protein_or_peptide / ID: 1
Details: Mature human RS1 with a C-terminal hexahistidine tag
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: STEDEGEDPW YQKACKCDCQ GGPNALWSAG ATSLDCIPEC PYHKPLGFES GEVTPDQITC SNPEQYVGWY SSWTANKARL NSQGFGCAWL SKFQDSSQWL QIDLKEIKVI SGILTQGRCD IDEWMTKYSV QYRTDERLNW IYYKDQTGNN RVFYGNS DR TSTVQNLLRP ...String:
STEDEGEDPW YQKACKCDCQ GGPNALWSAG ATSLDCIPEC PYHKPLGFES GEVTPDQITC SNPEQYVGWY SSWTANKARL NSQGFGCAWL SKFQDSSQWL QIDLKEIKVI SGILTQGRCD IDEWMTKYSV QYRTDERLNW IYYKDQTGNN RVFYGNS DR TSTVQNLLRP PIISRFIRLI PLGWHVRIAI RMELLECVSK CAHHHHHH

UniProtKB: Retinoschisin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMNaHPO4Sodium phosphate
500.0 mMNaClSodium chloride
200.0 mMC3H4N2Imidazole
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 1136 / Average exposure time: 0.25 sec. / Average electron dose: 0.66 e/Å2 / Details: 30 degree tilted specimen
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.23 µm / Calibrated defocus min: 1.04 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 26702
Startup modelType of model: EMDB MAP
EMDB ID:

6425


Details: Limited to 20 angstrom
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Bsoft (ver. 1.9)
Details: Reconstructed to 3 angstrom, low-pass filtered to 10 angstrom. Symmetrized two-fold (z-axis) and along screw-axis (x-axis).
Number images used: 18646
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Bsoft (ver. 1.9)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Bsoft (ver. 1.9)
FSC plot (resolution estimation)

+
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