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- PDB-2v6h: Crystal structure of the C1 domain of cardiac myosin binding protein-C -

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Basic information

Entry
Database: PDB / ID: 2v6h
TitleCrystal structure of the C1 domain of cardiac myosin binding protein-C
ComponentsMYOSIN-BINDING PROTEIN C, CARDIAC-TYPE
KeywordsCELL ADHESION / PHOSPHORYLATION / MYBP-C C1 DOMAIN / DISEASE MUTATION / MUSCLE REGULATION / IGI DOMAIN STRUCTURE / MUSCLE PROTEIN / CARDIOMYOPATHY / THICK FILAMENT / IMMUNOGLOBULIN DOMAIN / HYPERTROPIC CARDIOMYOPATHY / POLYMORPHISM / ACTIN-BINDING
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 / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle ...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 / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / myosin binding / sarcomere organization / 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. / Fibronectin type III ...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 / MAD / Resolution: 1.55 Å
AuthorsGovata, L. / Carpenter, L. / Da Fonseca, P.C.A. / Helliwell, J.R. / Rizkallah, P.J. / Flashman, E. / Chayen, N.E. / Redwood, C. / Squire, J.M.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: Crystal structure of the C1 domain of cardiac myosin binding protein-C: implications for hypertrophic cardiomyopathy.
Authors: Govada, L. / Carpenter, L. / da Fonseca, P.C. / Helliwell, J.R. / Rizkallah, P. / Flashman, E. / Chayen, N.E. / Redwood, C. / Squire, J.M.
History
DepositionJul 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
Water3,063170
1
A: MYOSIN-BINDING PROTEIN C, CARDIAC-TYPE

A: MYOSIN-BINDING PROTEIN C, CARDIAC-TYPE


Theoretical massNumber of molelcules
Total (without water)24,0992
Polymers24,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area2260 Å2
ΔGint-5.1 kcal/mol
Surface area13350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.848, 48.848, 95.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1082-

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: C1 DOMAIN, RESIDUES 151-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: CARDIAC / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q14896
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE C1 DOMAIN IS A 105 AMINO ACIDS PORTION.

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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: 2.4 Å3/Da / Density % sol: 48.83 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: HANGING DROP; 20 C; 18%PEG, 0.1M BUFFER, PH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MONO AND MIRROR
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 16401 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4
Reflection shellResolution: 1.45→1.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data reduction
SOLVEphasing
RESOLVEphasing
CNSphasing
REFMACphasing
SHELXL-97phasing
Cootmodel building
SHELXL-97refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.55→10 Å / Num. parameters: 4050 / Num. restraintsaints: 3548 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE STRUCTURE WAS SOLVED USING THREE - WAVELENGTH MAD DATA AT SRS 10.1 TO A RESOLUTION LIMIT OF 2.4ANGSTROM. THE DATA FOR REFINEMENT IS AS DETAILED MEASURED ON SRS 14.1. THE PROTEIN ...Details: THE STRUCTURE WAS SOLVED USING THREE - WAVELENGTH MAD DATA AT SRS 10.1 TO A RESOLUTION LIMIT OF 2.4ANGSTROM. THE DATA FOR REFINEMENT IS AS DETAILED MEASURED ON SRS 14.1. THE PROTEIN COORDINATES OVERALL 'CRUICKSHANK DIFFRACTION PRECISION INDICATOR (DPI)' 0.0982 ANGSTROM (BASED ON RFACTOR) AND 0.1074 ANGSTROM (BASED ON THE RFREE).
RfactorNum. reflection% reflectionSelection details
Rfree0.241 652 5 %RANDOM
obs0.184 -84 %-
all-12687 --
Refine analyzeNum. disordered residues: 5 / Occupancy sum non hydrogen: 985.5
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 170 986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0

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