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- PDB-5wlz: Crystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 5wlz
TitleCrystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac Myosin Fused to Xrcc4
ComponentsDNA repair protein XRCC4,Myosin-7
KeywordsMOTOR PROTEIN / Myosin / Xrcc4 / 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-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 / SUMOylation of DNA damage response and repair proteins / striated muscle contraction / 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 / 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 / : / : / : / 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: 3.5 Å
AuthorsAndreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111237 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod.
Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
C: DNA repair protein XRCC4,Myosin-7
D: DNA repair protein XRCC4,Myosin-7
A: DNA repair protein XRCC4,Myosin-7
B: DNA repair protein XRCC4,Myosin-7


Theoretical massNumber of molelcules
Total (without water)98,0194
Polymers98,0194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-100 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.290, 102.940, 136.457
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
DNA repair protein XRCC4,Myosin-7 / 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: 24504.676 Da / Num. of mol.: 4
Fragment: UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Mutation: E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: Q13426, UniProt: P12883

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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: 3.1 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8-10% methyl-ether polyethylene glycol (MEPEG) 5K, 300 mM glycine, bis-tris propane pH 7.0, 1.5-3.0% (w/v) jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 16299 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 17.1
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 808 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 3.5→44.068 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.2495 785 5.01 %
Rwork0.2135 --
obs0.2154 15666 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→44.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 0 0 6360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026448
X-RAY DIFFRACTIONf_angle_d0.4238663
X-RAY DIFFRACTIONf_dihedral_angle_d13.0553965
X-RAY DIFFRACTIONf_chiral_restr0.034987
X-RAY DIFFRACTIONf_plane_restr0.0021108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.71940.30881280.26542421X-RAY DIFFRACTION99
3.7194-4.00640.29281290.23722434X-RAY DIFFRACTION100
4.0064-4.40920.2211280.20662448X-RAY DIFFRACTION100
4.4092-5.04650.2511310.18232481X-RAY DIFFRACTION100
5.0465-6.3550.26151310.23522490X-RAY DIFFRACTION100
6.355-44.0710.20251380.18672607X-RAY DIFFRACTION100
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)
11.82140.88380.26453.51221.34143.46950.0368-0.4162-0.49160.7877-0.09890.06060.4554-0.07790.0510.6449-0.0066-0.03730.16590.19560.31081.315114.0921-12.4891
20.26080.34350.30030.86830.97433.0671-0.43390.3745-0.1026-0.4110.0055-0.0995-1.28310.33990.23220.4324-0.1164-0.040.27580.01040.3406-1.948530.074-64.5758
31.9874-0.96730.95594.4461-1.53433.34960.1066-0.19990.47320.39070.0142-0.2095-0.09980.2431-0.08060.4178-0.05780.0550.1448-0.15090.20724.749752.1553-12.9772
4-0.04040.18720.3520.3881.14974.5555-0.25330.2215-0.0974-0.0754-0.13230.30430.69070.1896-0.5890.4163-0.16260.00560.60390.00720.2126-1.63228.9568-62.1535
54.13640.5980.37364.58390.49433.8526-0.0679-0.05550.4678-0.1514-0.1580.0051-0.45030.08690.12930.03010.06280.00420.10790.03260.2857-19.554525.4912-31.6425
69.17294.84982.65318.16643.08313.89310.176-0.61370.30960.3368-0.0165-0.0368-0.3791-0.2728-0.1430.46770.13880.14960.1303-0.02360.2155-23.209727.3535-24.6098
70.15810.3117-0.37340.662-0.27951.4461-0.1374-0.1933-0.4237-0.1956-0.2408-0.41940.07240.7873-0.09210.25630.0650.05580.2762-0.06410.569223.18796.7303-44.73
83.0289-2.0047-0.19134.9213-0.62071.9687-0.02490.0347-0.3189-0.24670.10780.37770.5807-0.1927-0.0240.2399-0.13890.13390.0373-0.01470.2211-19.1865-10.7243-31.895
96.4208-3.5838-4.70055.72973.44524.02640.20030.8904-0.9649-0.4187-1.02971.0704-0.0472-1.04050.45010.4356-0.1692-0.2550.3964-0.00620.6575-26.7021-14.1447-36.0248
103.5481-0.1883-2.54020.40180.13662.20470.365-0.12850.7778-0.2443-0.1607-0.273-0.31480.7127-0.35380.23730.19570.17890.43970.02120.442921.65689.4722-43.8868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -1 through 118 )
2X-RAY DIFFRACTION2chain 'C' and (resid 119 through 1748 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 118 )
4X-RAY DIFFRACTION4chain 'D' and (resid 119 through 1745 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 118 )
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 1739 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 1739 )

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