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- PDB-3hsm: Crystal structure of distal N-terminal beta-trefoil domain of Rya... -

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Basic information

Entry
Database: PDB / ID: 3hsm
TitleCrystal structure of distal N-terminal beta-trefoil domain of Ryanodine Receptor type 1
ComponentsRyanodine receptor 1
KeywordsSIGNALING PROTEIN / beta-trefoil / Calcium / Calcium channel / Calcium transport / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Receptor / S-nitrosylation / Transmembrane / Transport
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 / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis ...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 / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAmador, F.J. / Liu, S. / Ishiyama, N. / Plevin, M.J. / Wilson, A. / MacLennan, D.H. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of type I ryanodine receptor amino-terminal beta-trefoil domain reveals a disease-associated mutation "hot spot" loop
Authors: Amador, F.J. / Liu, S. / Ishiyama, N. / Plevin, M.J. / Wilson, A. / MacLennan, D.H. / Ikura, M.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)46,5502
Polymers46,5502
Non-polymers00
Water70339
1
A: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)23,2751
Polymers23,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ryanodine receptor 1


Theoretical massNumber of molelcules
Total (without water)23,2751
Polymers23,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.597, 35.299, 78.940
Angle α, β, γ (deg.)90.000, 99.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ryanodine receptor 1 / / RYR-1 / RyR1 / Skeletal muscle-type ryanodine receptor / Skeletal muscle calcium release channel


Mass: 23275.230 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET232a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11716
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MES, 0.1M MgCl2, 24% PEG 3350, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 14141 / Num. obs: 13915 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.028 / Net I/σ(I): 14.938
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.251 / Num. unique all: 1313 / Χ2: 0.954 / % possible all: 94.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.216 / Packing: 0.29
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral97.8 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XZZ

1xzz


Resolution: 2.5→30.87 Å / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1317 9.7 %RANDOM
Rwork0.229 ---
all-13645 --
obs-12895 94.5 %-
Solvent computationBsol: 53.441 Å2
Displacement parametersBiso max: 89.05 Å2 / Biso mean: 46.178 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1--18.892 Å20 Å25.435 Å2
2--5.361 Å20 Å2
3---13.531 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 0 39 2573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6851.5
X-RAY DIFFRACTIONc_scbond_it2.2312
X-RAY DIFFRACTIONc_mcangle_it2.9312
X-RAY DIFFRACTIONc_scangle_it3.3662.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.338 122 -
Rwork0.283 --
obs-1425 85.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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