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- PDB-4xa4: Crystal Structure of the coiled-coil surrounding Skip 3 of MYH7 -

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Basic information

Entry
Database: PDB / ID: 4xa4
TitleCrystal Structure of the coiled-coil surrounding Skip 3 of MYH7
ComponentsXrcc4-MYH7(1551-1609) chimera protein
KeywordsMOTOR PROTEIN / Myosin / coiled coil / skip residue / fusion / Gp7 / EB1 / MYH7 / Cardiac
Function / homology
Function and homology information


FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA-dependent protein kinase-DNA ligase 4 complex / muscle myosin complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction ...FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA-dependent protein kinase-DNA ligase 4 complex / muscle myosin complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / protein localization to site of double-strand break / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / cellular response to lithium ion / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / 2-LTR circle formation / myofibril / response to X-ray / skeletal muscle contraction / striated muscle contraction / SUMOylation of DNA damage response and repair proteins / ATP metabolic process / cardiac muscle contraction / stress fiber / regulation of heart rate / muscle contraction / sarcomere / Nonhomologous End-Joining (NHEJ) / base-excision repair / double-strand break repair via nonhomologous end joining / Z disc / actin filament binding / double-strand break repair / site of double-strand break / calmodulin binding / enzyme binding / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Myosin-7 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.327 Å
AuthorsTaylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinz, N.T. / Qiang, C. / Leinwand, L.A. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL111237 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly.
Authors: Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinze, N.T. / Cui, Q. / Leinwand, L.A. / Rayment, I.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Xrcc4-MYH7(1551-1609) chimera protein
B: Xrcc4-MYH7(1551-1609) chimera protein


Theoretical massNumber of molelcules
Total (without water)47,6212
Polymers47,6212
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-47 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.548, 90.195, 102.717
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 Xrcc4-MYH7(1551-1609) chimera protein / chimera protein of DNA repair protein XRCC4 and Myosin-7


Mass: 23810.619 Da / Num. of mol.: 2
Fragment: UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13426, UniProt: P12883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.65 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) polyethylene glycol 1500, 250 mM tetramethylammonium chloride, 100 mM 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.327→50 Å / Num. obs: 22289 / % possible obs: 99 % / Redundancy: 7.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 32.9 / Net I/σ(I): 23.4
Reflection shellResolution: 2.327→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 8.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 2.327→34.542 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1144 5.13 %Random Selection
Rwork0.2159 ---
obs0.2188 22285 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.327→34.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 0 38 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093257
X-RAY DIFFRACTIONf_angle_d1.0874377
X-RAY DIFFRACTIONf_dihedral_angle_d17.1391231
X-RAY DIFFRACTIONf_chiral_restr0.041481
X-RAY DIFFRACTIONf_plane_restr0.004571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3265-2.43240.33921480.24712556X-RAY DIFFRACTION98
2.4324-2.56060.28441500.24992592X-RAY DIFFRACTION100
2.5606-2.7210.32541530.25752629X-RAY DIFFRACTION100
2.721-2.93090.31381460.2552613X-RAY DIFFRACTION100
2.9309-3.22570.28451410.25142642X-RAY DIFFRACTION100
3.2257-3.6920.27451380.21622653X-RAY DIFFRACTION100
3.692-4.64970.2591300.18752702X-RAY DIFFRACTION100
4.6497-34.54570.23531380.18872754X-RAY DIFFRACTION97

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