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- PDB-5cj0: Crystal Structure of Amino Acids 1631-1692 of MYH7 -

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Basic information

Entry
Database: PDB / ID: 5cj0
TitleCrystal Structure of Amino Acids 1631-1692 of MYH7
ComponentsXrcc4-MYH7-(1631-1692) chimera protein
KeywordsMOTOR PROTEIN / Myosin / coiled-coil
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 ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...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 ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / protein localization to site of double-strand break / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / myosin complex / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / cellular response to lithium ion / 2-LTR circle formation / skeletal muscle contraction / response to X-ray / striated muscle contraction / SUMOylation of DNA damage response and repair proteins / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Nonhomologous End-Joining (NHEJ) / Z disc / double-strand break repair via nonhomologous end joining / double-strand break repair / actin filament binding / site of double-strand break / calmodulin binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail ...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 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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: 2.3 Å
AuthorsKorkmaz, N.E. / Taylor, K.C. / Andreas, M.P. / Ajay, G. / Heinze, N.T. / Cui, Q. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL111237 United States
National Science Foundation (NSF, United States)CHE1300209 United States
CitationJournal: Proteins / Year: 2016
Title: A composite approach towards a complete model of the myosin rod.
Authors: Korkmaz, E.N. / Taylor, K.C. / Andreas, M.P. / Ajay, G. / Heinze, N.T. / Cui, Q. / Rayment, I.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xrcc4-MYH7-(1631-1692) chimera protein
B: Xrcc4-MYH7-(1631-1692) chimera protein


Theoretical massNumber of molelcules
Total (without water)46,4662
Polymers46,4662
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-50 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.006, 44.355, 74.664
Angle α, β, γ (deg.)90.000, 108.190, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 1689 / Label seq-ID: 4 - 204

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Xrcc4-MYH7-(1631-1692) chimera protein / X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform ...X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 23233.059 Da / Num. of mol.: 2
Fragment: UNP Q13426 residues 2-142, UNP P12883 residues 1631-1692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Plasmid: pET31b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13426, UniProt: P12883
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% (w/v) MEPEG 5000, 200 mM glycine, 100 mM bistrispropane pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2014
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 29079 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 40.2
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.45 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 2.3→49.864 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1404 5 %
Rwork0.2162 26685 -
obs0.2173 28089 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.03 Å2 / Biso mean: 63.3635 Å2 / Biso min: 28.74 Å2
Refinement stepCycle: final / Resolution: 2.3→49.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 108 3293
Biso mean---53.82 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043237
X-RAY DIFFRACTIONf_angle_d0.784360
X-RAY DIFFRACTIONf_chiral_restr0.026490
X-RAY DIFFRACTIONf_plane_restr0.011571
X-RAY DIFFRACTIONf_dihedral_angle_d14.2241220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1804X-RAY DIFFRACTION5.35TORSIONAL
12B1804X-RAY DIFFRACTION5.35TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38230.34911480.287226332781100
2.3823-2.47760.28991320.277126722804100
2.4776-2.59040.29751360.280226312767100
2.5904-2.7270.32461420.268226462788100
2.727-2.89780.28621440.251326522796100
2.8978-3.12150.32031360.256126832819100
3.1215-3.43560.23271370.235126562793100
3.4356-3.93250.24721420.2126782820100
3.9325-4.95390.17031410.163727022843100
4.9539-49.87570.20811460.19412732287898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0849-0.918-0.23514.49531.52614.65980.04790.6091-0.0053-0.8079-0.3056-0.1248-0.03370.16390.23940.43330.0950.08870.4669-0.03020.367961.7874-8.396623.1964
24.0101-0.2921.8362-0.08270.15541.10850.4043-0.1978-0.0187-0.0302-0.25440.05250.2463-0.2385-0.13110.4558-0.0457-0.07930.427-0.01230.49229.2572-2.037423.1747
34.3488-1.4497-1.76074.86182.486.4022-0.1327-0.4202-0.14350.7230.09860.11910.3492-0.10520.02820.45710.0285-0.02470.3272-0.03350.299452.58233.814958.7963
44.17830.57783.7127-0.10330.39232.3911-0.1288-0.41360.7195-0.0676-0.15930.0239-0.0609-0.20910.28150.380.0096-0.04750.51390.0340.50789.6459-1.635823.3894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 1689 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 118 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 119 through 1689 )B0

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