[English] 日本語
Yorodumi
- EMDB-1274: Structure of Ca2+ release channel at 14 A resolution. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1274
TitleStructure of Ca2+ release channel at 14 A resolution.
Map dataThe map is rendered from the cytoplasmic side (top view) along 4-fold axis of the protein
Sample
  • Sample: ryanodine receptor 1
  • Protein or peptide: Ryanodine receptor type 1
Function / homologyryanodine-sensitive calcium-release channel activity / RIH domain
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsSerysheva II / Hamilton SL / Chiu W / Ludtke SJ
CitationJournal: J Mol Biol / Year: 2005
Title: Structure of Ca2+ release channel at 14 A resolution.
Authors: Irina I Serysheva / Susan L Hamilton / Wah Chiu / Steven J Ludtke /
Abstract: The 14 A resolution structure of the 2.3 MDa Ca2+ release channel (also known as RyR1) was determined by electron cryomicroscopy and single particle reconstruction. This structure was produced using ...The 14 A resolution structure of the 2.3 MDa Ca2+ release channel (also known as RyR1) was determined by electron cryomicroscopy and single particle reconstruction. This structure was produced using collected data used for our previous published structures at 22-30 A resolution, but now taking advantage of recent algorithmic improvements in the EMAN software suite. This improved map clearly exhibits more structural detail and allows better defined docking of computationally predicted structural domain folds. Using sequence-based fold recognition, the N-terminal region of RyR1, residues 216-572, was predicted to have significant structural similarity with the IP3-binding core region of the type 1 IP3R. This putative structure was computationally localized to the clamp-shaped region of RyR1, which has been implicated to have a regulatory role in the channel activity.
History
DepositionJan 17, 2006-
Header (metadata) releaseOct 12, 2006-
Map releaseOct 12, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1274.gif

Downloads & links

-
Map

FileDownload / File: emd_1274.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map is rendered from the cytoplasmic side (top view) along 4-fold axis of the protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.67 Å/pix.
x 100 pix.
= 462.033 Å		4.67 Å/pix.
x 100 pix.
= 462.033 Å		4.67 Å/pix.
x 100 pix.
= 462.033 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.667 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.366 / Movie #1: 1
Minimum - Maximum-2.02439 - 3.1551
Average (Standard dev.)0.0582325 (±0.324772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 462.033 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.6674.6674.667
M x/y/z999999
origin x/y/z0.0000.0000.000
length x/y/z462.033462.033462.033
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-2.0243.1550.058

-
Supplemental data

-
Sample components

-
Entire : ryanodine receptor 1

EntireName: ryanodine receptor 1
Components
  • Sample: ryanodine receptor 1
  • Protein or peptide: Ryanodine receptor type 1

-
Supramolecule #1000: ryanodine receptor 1

SupramoleculeName: ryanodine receptor 1 / type: sample / ID: 1000
Details: The sample was purified after solubiliztion with detergent from rabbit skeletal muscle
Oligomeric state: Homotetramer / Number unique components: 1
Molecular weightTheoretical: 565 KDa

-
Macromolecule #1: Ryanodine receptor type 1

MacromoleculeName: Ryanodine receptor type 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Skeletal muscle calcium release channel / Details: detergent solubilized membrane protein / Number of copies: 4 / Oligomeric state: Homotetramer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: White New Zealand / synonym: rabbit / Tissue: fast twitch skeletal muscle / Cell: muscle cell / Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane
Molecular weightExperimental: 565 KDa
SequenceGO: ryanodine-sensitive calcium-release channel activity / InterPro: RIH domain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 300 mM KCl, 1 mM DTT, 0.4 % CHAPS, 5% sucrose, 1mM EGTA, 20 mM Mops
GridDetails: thin carbon film support by holey carbon 400 mesh Cu grid
VitrificationCryogen name: ETHANE / Chamber temperature: 101 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual Plunger / Method: Blot for about 3 second before plunging

-
Electron microscopy

MicroscopeJEOL 1200EX
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 5.6 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 109 K / Max: 110 K / Average: 109 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 300,000X
DetailsElectron Microscope JEM2010F
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 4.667 µm / Number real images: 52 / Average electron dose: 7 e/Å2

-
Image processing

CTF correctionDetails: CTF correction of each micrograph
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 22000

+
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