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- PDB-3rqr: Crystal structure of the RYR domain of the rabbit ryanodine receptor -

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Basic information

Entry
Database: PDB / ID: 3rqr
TitleCrystal structure of the RYR domain of the rabbit ryanodine receptor
Components
  • (UNK)(UNK)(UNK)(UNK)
  • Ryanodine receptor 1
KeywordsMETAL TRANSPORT / RYANODINE RECEPTOR / RYR domain
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 / organelle membrane / cellular response to caffeine / 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 / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / 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
Globin-like - #160 / : / 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 ...Globin-like - #160 / : / 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. / Globin-like / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsNair, U.B. / Li, W. / Dong, A. / Walker, J.R. / Gramolini, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Febs J. / Year: 2012
Title: Structural determination of the phosphorylation domain of the ryanodine receptor.
Authors: Sharma, P. / Ishiyama, N. / Nair, U. / Li, W. / Dong, A. / Miyake, T. / Wilson, A. / Ryan, T. / Maclennan, D.H. / Kislinger, T. / Ikura, M. / Dhe-Paganon, S. / Gramolini, A.O.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999Author state that Chain U2047-U2050 is likely belong to chain A but due to the poor quality of the ...Author state that Chain U2047-U2050 is likely belong to chain A but due to the poor quality of the electron density, they can not assign the correct sequence to them. So they are modeled as UNK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ryanodine receptor 1
U: (UNK)(UNK)(UNK)(UNK)


Theoretical massNumber of molelcules
Total (without water)26,8382
Polymers26,8382
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-11 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.770, 68.770, 91.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 26479.762 Da / Num. of mol.: 1 / Fragment: Residues 2733-2940
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11716
#2: Protein/peptide (UNK)(UNK)(UNK)(UNK)


Mass: 358.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 1.2M Na Citrate, 100mM Tris pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU FR-E+ DW12.29
SYNCHROTRONAPS 19-ID21.00724
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEApr 10, 2011VARIMAX CR
ADSC QUANTUM 3152CCDApr 21, 2011SI(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1VARIMAX CRSADMx-ray1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.291
21.007241
ReflectionResolution: 2.16→50 Å / Num. obs: 12353 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 31.33 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 19.7
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2 / Rsym value: 0.846 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
SOLVEphasing
RESOLVEmodel building
BUSTER2.8.0refinement
Coot0.6model building
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→42.93 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 917 7.94 %RANDOM
Rwork0.231 ---
obs0.238 11546 --
all-12353 --
Displacement parametersBiso mean: 36.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.4322 Å20 Å20 Å2
2---0.4322 Å20 Å2
3---0.8644 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.16→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 0 118 1648
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011587HARMONIC1.6
X-RAY DIFFRACTIONt_angle_deg1.032156HARMONIC1.6
X-RAY DIFFRACTIONt_dihedral_angle_d537SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes226HARMONIC5
X-RAY DIFFRACTIONt_it1587HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion18.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion204SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1867SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.37 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3018 179 7.29 %
Rwork0.2596 2278 -
all0.2626 2457 -
Refinement TLS params.Method: refined / Origin x: 59.8992 Å / Origin y: 21.9141 Å / Origin z: 41.0532 Å
111213212223313233
T-0.0723 Å20.006 Å2-0.0143 Å2--0.0963 Å2-0.0181 Å2---0.0453 Å2
L1.0611 °20.3556 °20.2333 °2-1.8479 °20.0639 °2--0.6615 °2
S0.0812 Å °-0.0222 Å °0.0414 Å °0.1762 Å °-0.0341 Å °-0.1627 Å °0.0855 Å °-0.0451 Å °-0.0471 Å °
Refinement TLS groupSelection details: { A|* }

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