[English] 日本語
Yorodumi
- PDB-9l91: The crystal structure of human RyR3 Repeat12 domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l91
TitleThe crystal structure of human RyR3 Repeat12 domain in complex with Azumolene and AMP-PCP
ComponentsRyanodine receptor 3
KeywordsMEMBRANE PROTEIN / Repeat12 domain / Azumolene / AMP-PCP / ryanodine receptor
Function / homology
Function and homology information


calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to caffeine / cellular response to ATP / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol ...calcium-induced calcium release activity / cellular response to magnesium ion / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to caffeine / cellular response to ATP / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcolemma / calcium ion transmembrane transport / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / calcium ion transport / protein homotetramerization / calmodulin binding / calcium ion 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 / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
: / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Ryanodine receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHadiatullah, H. / Lin, L. / Yuchi, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural Basis for the Modulation of Ryanodine Receptor by Dantrolene and Azumolene
Authors: Hadiatullah, H. / Lin, L. / Yuchi, Z.
History
DepositionDec 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ryanodine receptor 3
A: Ryanodine receptor 3
C: Ryanodine receptor 3
D: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6838
Polymers99,9744
Non-polymers1,7094
Water84747
1
B: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8483
Polymers24,9941
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ryanodine receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8483
Polymers24,9941
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ryanodine receptor 3


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.666, 59.960, 60.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ryanodine receptor 3 / RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / ...RYR-3 / RyR3 / Brain ryanodine receptor-calcium release channel / Brain-type ryanodine receptor / Type 3 ryanodine receptor


Mass: 24993.588 Da / Num. of mol.: 4 / Fragment: Repeat12 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR3, HBRR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15413
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-A1L7B / Azumolene


Mass: 349.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9BrN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.4M sodium chloride, 0.1M HEPES pH 7.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→130.83 Å / Num. obs: 20109 / % possible obs: 96.2 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Χ2: 1.1 / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.862 / Num. unique obs: 2894 / CC1/2: 0.901 / Rpim(I) all: 0.285 / Rrim(I) all: 0.91 / Χ2: 0.79

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→130.83 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3167 1966 -
Rwork0.268 --
obs0.2813 19335 96.33 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→130.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 104 47 5869

+
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