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- PDB-2bcx: Crystal structure of calmodulin in complex with a ryanodine recep... -

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Basic information

Entry
Database: PDB / ID: 2bcx
TitleCrystal structure of calmodulin in complex with a ryanodine receptor peptide
Components
  • Calmodulin
  • Ryanodine receptor 1
KeywordsCALCIUM BINDING PROTEIN / EF-hand / type-2 turn
Function / homology
Function and homology information


CH domain binding / 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 / myosin binding / cellular response to caffeine ...CH domain binding / 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 / myosin binding / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / organelle membrane / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / enzyme regulator activity / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / 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 / protein-containing complex / ATP binding / identical protein binding / membrane
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. / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / 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 / Calmodulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsMaximciuc, A.A. / Shamoo, Y. / MacKenzie, K.R.
CitationJournal: Structure / Year: 2006
Title: Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode.
Authors: Maximciuc, A.A. / Putkey, J.A. / Shamoo, Y. / Mackenzie, K.R.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5086
Polymers20,3482
Non-polymers1604
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-77 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 44.100, 90.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM / Production host: Escherichia coli (E. coli) / References: UniProt: P62149
#2: Protein/peptide Ryanodine receptor 1 / Skeletal muscle-type ryanodine receptor / RyR1 / RYR-1 / Skeletal muscle calcium release channel


Mass: 3626.437 Da / Num. of mol.: 1 / Fragment: residues 3614-3643 / Source method: obtained synthetically
Details: synthetic peptide based on the sequence of rabbit ryanodine receptor 1
References: UniProt: P11716
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.863831 Å3/Da / Density % sol: 34.006889 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 23% PEG 4000, 0.1 M sodium acetate, 5 mM DTT, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 8.3 % / Number: 4773 / Rmerge(I) obs: 0.055 / Χ2: 1.917 / D res high: 2.65 Å / D res low: 50 Å / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.71509410.0483.0627.8
4.535.7110010.0512.7358.5
3.964.5310010.0442.2478.6
3.63.9610010.0492.2528.6
3.343.610010.061.98.6
3.143.3410010.061.5968.7
2.983.1410010.0711.4698.7
2.852.9810010.0771.2868.4
2.742.8510010.0881.1998.6
2.652.7493.910.0951.136.7
ReflectionResolution: 2→39.66 Å / Num. all: 19856 / Num. obs: 10802 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.73 % / Rmerge(I) obs: 0.038 / Χ2: 1.13 / Net I/σ(I): 23.2 / Scaling rejects: 561
Reflection shellResolution: 2→2.07 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 7.8 / Num. measured obs: 42 / Χ2: 1.18 / % possible all: 99.9

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.6516.32003774938
ANO_12.6516.321.414037730
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_17.54-16.320012489
ISO_15.64-7.540021394
ISO_14.7-5.640027097
ISO_14.11-4.70033196
ISO_13.7-4.110037590
ISO_13.39-3.70042192
ISO_13.15-3.390045593
ISO_12.95-3.150049193
ISO_12.79-2.9500535101
ISO_12.65-2.790055993
ANO_17.54-16.322.10601240
ANO_15.64-7.542.66702130
ANO_14.7-5.642.13802700
ANO_14.11-4.71.67403310
ANO_13.7-4.111.48603750
ANO_13.39-3.71.35804210
ANO_13.15-3.391.19104550
ANO_12.95-3.151.09904910
ANO_12.79-2.951.03405350
ANO_12.65-2.790.90505580
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
122.4146.8425.38S201
232.9373.87515.888S200.936
315.57215.773.521S200.927
433.696-3.8696.987S200.874
513.0484.309-2.8S200.45
631.242-9.07823.445S200.384
76.4941.45-12.206S200.35
839.094-9.99815.267S200.327
910.3431.363-3.014S200.319
1025.756-11.6593.356S200.212
1122.078-9.66523.307S200.21
1213.162-10.45818.089S200.195
1342.117-11.6217.146S200.192
1421.367-16.5132.661S200.191
1523.589-9.16516.565S200.131
163.649-1.394-7.989S200.105
1718.8115.7231.623S200.079

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
SHARPphasing
SOLOMONphasing
CNS1.1refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→9.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 989785.438 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1009 5.1 %RANDOM
Rwork0.213 ---
all0.214 19647 --
obs0.214 10802 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.426 Å2 / ksol: 0.453 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å20 Å2
2--6.31 Å20 Å2
3----3.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 4 80 1431
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 174 5.4 %
Rwork0.223 3050 -
all-3224 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2ion.topion.param
X-RAY DIFFRACTION3water.topwater.param

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