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- PDB-5cj4: Crystal Structure of Amino Acids 1562-1622 of MYH7 -

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Basic information

Entry
Database: PDB / ID: 5cj4
TitleCrystal Structure of Amino Acids 1562-1622 of MYH7
ComponentsXrcc4-MYH7-(1562-1622) 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 / stress fiber / ATP metabolic process / 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: 3.102 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-(1562-1622) chimera protein
B: Xrcc4-MYH7-(1562-1622) chimera protein
C: Xrcc4-MYH7-(1562-1622) chimera protein
D: Xrcc4-MYH7-(1562-1622) chimera protein


Theoretical massNumber of molelcules
Total (without water)96,4294
Polymers96,4294
Non-polymers00
Water362
1
A: Xrcc4-MYH7-(1562-1622) chimera protein
B: Xrcc4-MYH7-(1562-1622) chimera protein


Theoretical massNumber of molelcules
Total (without water)48,2152
Polymers48,2152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-44 kcal/mol
Surface area23260 Å2
MethodPISA
2
C: Xrcc4-MYH7-(1562-1622) chimera protein
D: Xrcc4-MYH7-(1562-1622) chimera protein


Theoretical massNumber of molelcules
Total (without water)48,2152
Polymers48,2152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-46 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.145, 57.285, 112.100
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MLYMLYchain AAA1 - 16154 - 201
2ARGARGchain BBB1 - 16084 - 194
3GLUGLUchain CCC1 - 16194 - 205
4LEULEUchain DDD1 - 16124 - 198

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Components

#1: Protein
Xrcc4-MYH7-(1562-1622) 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: 24107.324 Da / Num. of mol.: 4 / Fragment: UNP Q13426 residues 2-144, UNP P12883 1562-1622
Source method: isolated from a genetically manipulated source
Details: Lysines were reductively alkylated to dimethyllysine.
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / 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.: 2 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% (w/v) PEG 4000, 500 mM NaCl, 100 mM triethanolamine pH 8.0.

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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: 3.1→50 Å / Num. obs: 19051 / % possible obs: 99.1 % / Redundancy: 6 % / Biso Wilson estimate: 66.66 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.2
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 3.102→49.923 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 948 5 %
Rwork0.2432 18011 -
obs0.245 18959 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.26 Å2 / Biso mean: 81.9698 Å2 / Biso min: 35.56 Å2
Refinement stepCycle: final / Resolution: 3.102→49.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 0 2 6343
Biso mean---61.58 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046433
X-RAY DIFFRACTIONf_angle_d0.7418655
X-RAY DIFFRACTIONf_chiral_restr0.032940
X-RAY DIFFRACTIONf_plane_restr0.0031098
X-RAY DIFFRACTIONf_dihedral_angle_d14.5862447
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3056X-RAY DIFFRACTION12.111TORSIONAL
12B3056X-RAY DIFFRACTION12.111TORSIONAL
13C3056X-RAY DIFFRACTION12.111TORSIONAL
14D3056X-RAY DIFFRACTION12.111TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1016-3.26510.32411320.28442520265298
3.2651-3.46960.32361340.28542564269899
3.4696-3.73740.29231360.25332579271599
3.7374-4.11330.24931350.24932562269799
4.1133-4.70820.25711350.21622572270799
4.7082-5.93020.26941380.2392587272598
5.9302-49.92920.28841380.2332627276598
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)
13.7725-0.3135-1.42931.80221.96345.21350.00290.3266-0.1993-0.2331-0.1334-0.1818-0.14590.9860.14840.45760.01-0.03190.72330.04670.535896.3493-17.7439110.69
26.16560.90322.5315-0.23730.14781.99950.21960.19031.49710.0922-0.75780.5431-0.22-0.50450.30040.47280.0961-0.19181.1474-0.17290.781469.4668-15.4385118.3763
37.16871.58991.87522.91551.13475.22380.687-0.7172-0.96250.327-0.4434-0.06251.1442-0.496-0.00550.6119-0.0064-0.07471.14180.00430.560519.8274-22.214989.8215
43.16640.2275-1.3872.2649-0.10074.37580.1073-0.4124-0.26650.305-0.36370.31820.4629-0.5090.10090.5017-0.17420.01890.6679-0.10140.668272.4945-22.9779135.0062
55.96120.22332.28012.87731.023.9635-0.0862-0.07680.9717-0.29320.13850.30220.3542-0.1289-0.25450.5127-0.0085-0.07090.9210.04320.563828.2548-16.307884.7998
63.4613-1.0392-2.15342.17940.94014.40880.05710.13750.281-0.32630.2343-0.0499-0.35690.1152-0.2140.5268-0.0785-0.05910.3972-0.01440.5013104.68339.377761.5806
71.01250.7805-0.82471.83491.07533.33390.0967-0.10860.5138-0.25490.1797-0.0516-0.01980.1667-0.13580.6369-0.0137-0.0290.40940.04910.45993.85528.555365.7969
82.92480.681-0.58052.25042.48491.6769-0.12830.15060.83910.0835-0.1980.2962-0.0650.30490.13560.7034-0.146-0.03330.83480.21840.506626.88920.465238.7101
94.4914-0.9013-1.8286-0.00280.28243.5608-0.2083-0.5317-0.04360.06390.23020.34150.1986-0.6775-0.05820.6087-0.0198-0.01440.8020.10020.698982.88395.448786.0213
108.95950.88652.40081.64660.49563.84060.5878-0.22930.27950.2863-0.34350.37160.90680.1699-0.04740.5269-0.0653-0.03440.76640.14690.591135.36194.730234.5294
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 1572 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1573 through 1614 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 1570 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1571 through 1608 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 89 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 91 through 1572 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 1573 through 1619 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 1572 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 1573 through 1612 )D0

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