[English] 日本語
Yorodumi
- EMDB-2751: Structure of the ryanodine receptor at resolution of 6.1 A in clo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2751
TitleStructure of the ryanodine receptor at resolution of 6.1 A in closed state
Map datareconstruction of rye reconstituted in lipid nanodiscs in closed state
Sample
  • Sample: Ryanodine receptor 1 (calcium release channel) from rabbit
  • Protein or peptide: Ryanodine receptor 1
Keywordscalcium binding / ion channel / muscular contraction / conformational changes.
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / outflow tract morphogenesis / toxic substance binding / striated muscle contraction / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / muscle contraction / cellular response to calcium ion / sarcoplasmic reticulum / sarcolemma / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEfremov RG / Leitner A / Aebersold R / Raunser S
CitationJournal: Nature / Year: 2015
Title: Architecture and conformational switch mechanism of the ryanodine receptor.
Authors: Rouslan G Efremov / Alexander Leitner / Ruedi Aebersold / Stefan Raunser /
Abstract: Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels ...Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels with a molecular mass of more than 2.2 megadaltons that are regulated by several factors, including ions, small molecules and proteins. Numerous mutations in RyRs have been associated with human diseases. The molecular mechanism underlying the complex regulation of RyRs is poorly understood. Using electron cryomicroscopy, here we determine the architecture of rabbit RyR1 at a resolution of 6.1 Å. We show that the cytoplasmic moiety of RyR1 contains two large α-solenoid domains and several smaller domains, with folds suggestive of participation in protein-protein interactions. The transmembrane domain represents a chimaera of voltage-gated sodium and pH-activated ion channels. We identify the calcium-binding EF-hand domain and show that it functions as a conformational switch allosterically gating the channel.
History
DepositionAug 6, 2014-
Header (metadata) releaseAug 13, 2014-
Map releaseDec 10, 2014-
UpdateJan 14, 2015-
Current statusJan 14, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4uwa
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2751-map-sna...

Downloads & links

-
Map

FileDownload / File: emd_2751.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of rye reconstituted in lipid nanodiscs in closed state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 384 pix.
= 545.28 Å		1.42 Å/pix.
x 384 pix.
= 545.28 Å		1.42 Å/pix.
x 384 pix.
= 545.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.443 / Movie #1: 0.7
Minimum - Maximum-2.49700332 - 3.86221123
Average (Standard dev.)0.00991019 (±0.11789458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 545.27997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z545.280545.280545.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ442626
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-2.4973.8620.010

-
Supplemental data

-
Segmentation: The mask used for calculating FSC

AnnotationThe mask used for calculating FSC
Fileemd_2751_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ryanodine receptor 1 (calcium release channel) from rabbit

EntireName: Ryanodine receptor 1 (calcium release channel) from rabbit
Components
  • Sample: Ryanodine receptor 1 (calcium release channel) from rabbit
  • Protein or peptide: Ryanodine receptor 1

-
Supramolecule #1000: Ryanodine receptor 1 (calcium release channel) from rabbit

SupramoleculeName: Ryanodine receptor 1 (calcium release channel) from rabbit
type: sample / ID: 1000 / Details: protein was reconstituted in lipid nanodiscs / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 2.26 MDa

-
Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Skeletal muscle calcium release channel / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: muscle / Organelle: Sarcoplasmic reticulum / Location in cell: Sarcoplasmic reticulum membrane
Molecular weightTheoretical: 2.26 MDa
SequenceUniProtKB: Ryanodine receptor 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Details: 10 mM MOPS, 200 mM NaCl, 1mM EGTA, 0.2% fluorinated octyl-maltoside
GridDetails: Quantifoil R 2/1 holey carbon grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: protein solution was applied on glow discharged grid and blotted for 4 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Cs0
TemperatureMin: 80 K
DateFeb 3, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2320 / Average electron dose: 20 e/Å2
Details: Images were collected automatically with CPU software and using movie mode with 7 frames per image.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000 / Cs: mm
Sample stageSpecimen holder: liquid nitorgen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsDefocus of the micrographs was determined in CTFFIND, particles were picked manually in E2BOXER, 3D reconstruction was calculated in RELION
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: OTHER / Software - Name: SPARX, RELION / Number images used: 25000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

2aox

SoftwareName: Chimera
DetailsThe domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4uwa:
Structure of the ryanodine receptor at resolution of 6.1 A in closed state

-
Atomic model buiding 2

Initial modelPDB ID:

4ert

SoftwareName: Chimera
DetailsThe domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4uwa:
Structure of the ryanodine receptor at resolution of 6.1 A in closed state

-
Atomic model buiding 3

Initial modelPDB ID:

2r9r

SoftwareName: Chimera
DetailsThe domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4uwa:
Structure of the ryanodine receptor at resolution of 6.1 A in closed state

+
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