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- PDB-3cx2: Crystal structure of the C1 domain of cardiac isoform of myosin b... -

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Basic information

Entry
Database: PDB / ID: 3cx2
TitleCrystal structure of the C1 domain of cardiac isoform of myosin binding protein-C at 1.3A
ComponentsMyosin-binding protein C, cardiac-type
KeywordsCONTRACTILE PROTEIN / myosin-binding protein / protonation states / Actin-binding / Cardiomyopathy / Cell adhesion / Disease mutation / Immunoglobulin domain / Muscle protein / Phosphoprotein / Polymorphism / Thick filament
Function / homology
Function and homology information


C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / A band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis ...C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / A band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / myosin binding / myosin heavy chain binding / ATPase activator activity / heart morphogenesis / cardiac muscle contraction / titin binding / sarcomere / actin binding / cell adhesion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
: / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...: / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myosin-binding protein C, cardiac-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.3 Å
AuthorsFisher, S.J. / Helliwell, J.R. / Khurshid, S. / Govada, L. / Redwood, C. / Squire, J.M. / Chayen, N.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: An investigation into the protonation states of the C1 domain of cardiac myosin-binding protein C
Authors: Fisher, S.J. / Helliwell, J.R. / Khurshid, S. / Govada, L. / Redwood, C. / Squire, J.M. / Chayen, N.E.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Aug 30, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin-binding protein C, cardiac-type


Theoretical massNumber of molelcules
Total (without water)12,0501
Polymers12,0501
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.848, 48.848, 95.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

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Components

#1: Protein Myosin-binding protein C, cardiac-type / Cardiac MyBP-C / C-protein / cardiac muscle isoform


Mass: 12049.611 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBPC3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14896
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Crystals were grown at 20 C using the hanging drop method with a 2 microlitre drop containing a 1:1 mixture of protein solution and crystallising solution consisting of 8.5% PEG 3350 and 0. ...Details: Crystals were grown at 20 C using the hanging drop method with a 2 microlitre drop containing a 1:1 mixture of protein solution and crystallising solution consisting of 8.5% PEG 3350 and 0.05M Hepes pH 6.8 over 500 microlitres of crystallising solution in the reservoir, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2006
RadiationMonochromator: double crystal Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 22822 / Num. obs: 26342 / % possible obs: 88.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.046 / Χ2: 1.612 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.3 / Χ2: 1.627 / % possible all: 33.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIR
Starting model: PDB entry 2V6H

2v6h


Resolution: 1.3→10 Å / Num. parameters: 9403 / Num. restraintsaints: 11538 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1184 -RANDOM
obs0.164 24006 84.2 %-
all-22822 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 22.271 Å2
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 176 1044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.065

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