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- PDB-5wme: Crystal Structure of Amino Acids 1729-1786 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 5wme
TitleCrystal Structure of Amino Acids 1729-1786 of Human Beta Cardiac Myosin Fused to Gp7 as Anti-Parallel Four-Helix Bundle
ComponentsCapsid assembly scaffolding protein,Myosin-7
KeywordsMOTOR PROTEIN / Myosin / Gp7 / Coiled-Coil
Function / homology
Function and homology information


viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding ...viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / virion assembly / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cardiac muscle contraction / stress fiber / regulation of heart rate / muscle contraction / sarcomere / Z disc / actin filament binding / calmodulin binding / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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. ...Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-7 / Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
A: Capsid assembly scaffolding protein,Myosin-7
B: Capsid assembly scaffolding protein,Myosin-7
C: Capsid assembly scaffolding protein,Myosin-7
D: Capsid assembly scaffolding protein,Myosin-7


Theoretical massNumber of molelcules
Total (without water)49,4194
Polymers49,4194
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-117 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.247, 72.960, 114.484
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsid assembly scaffolding protein,Myosin-7 / Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Myosin heavy ...Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 12354.793 Da / Num. of mol.: 4
Fragment: UNP P13848 residues 2-48, UNP P12883 residues 1729-1786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P12883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% (w/v) pentaerythritol ethoxylate 797, 150 mM ammonium thiocyanate, 100 mM sodium acetate pH 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17830 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 868 / % possible all: 97

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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: 1NO4

1no4


Resolution: 2.3→44.867 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.88
RfactorNum. reflection% reflection
Rfree0.2643 875 4.97 %
Rwork0.2242 --
obs0.2262 17620 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 0 51 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012929
X-RAY DIFFRACTIONf_angle_d0.3253930
X-RAY DIFFRACTIONf_dihedral_angle_d13.171893
X-RAY DIFFRACTIONf_chiral_restr0.028442
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.44430.31971450.25022781X-RAY DIFFRACTION98
2.4443-2.6330.25381460.26522747X-RAY DIFFRACTION99
2.633-2.89790.32511480.25782774X-RAY DIFFRACTION99
2.8979-3.31710.3131420.24752791X-RAY DIFFRACTION100
3.3171-4.17880.22541480.19282812X-RAY DIFFRACTION100
4.1788-44.87580.23621460.20362840X-RAY DIFFRACTION99
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)
14.7643-2.34835.1544.2207-4.50257.3460.44190.0777-0.5363-1.09190.40320.25110.8929-0.7843-0.78890.5587-0.050.05120.34740.05910.38328.7154-17.471224.5455
24.3003-4.56026.03174.2602-6.15652.4432-0.25460.12570.13960.2313-0.1127-0.2775-0.41750.62160.51690.2893-0.0625-0.01830.34850.09230.36914.4761.8182-13.3915
36.9054-0.10150.68676.2074-1.58699.10590.25530.1216-1.0469-0.1436-0.2653-0.32980.87610.80450.07250.21070.00180.02060.14980.01080.4307-21.759811.4354-86.3611
41.8743-0.74754.68070.5124-2.26797.9272-0.094-0.06350.03840.12030.05460.0833-0.3832-0.2990.01640.23670.08280.01910.3107-0.00620.2906-16.173310.1362-44.2607
56.92760.07181.37337.6031-0.84927.94850.0099-0.72150.22360.7072-0.2385-0.2743-0.1391-0.47250.1530.1211-0.0259-0.01130.1993-0.01640.2074-26.154824.2768-81.0628
60.708-1.33823.37871.66-3.95417.71890.07510.16620.1273-0.0335-0.2424-0.01670.08180.50830.15380.29420.10620.04360.41520.06290.2531-6.58865.3628-47.8618
79.6865-0.0792-3.05832.07821.67239.6027-0.272-0.11030.95560.6516-0.2845-0.8344-0.99881.21820.54191.1879-0.0725-0.48640.5030.15730.928815.4617-5.0127.3355
82.0014-1.42984.55951.2983-2.33468.3280.391-0.3961-0.39590.17720.39730.25670.3883-0.8956-0.51430.2679-0.09290.0390.31670.07160.2753-5.0328-3.5105-11.3343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 1772 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 1772 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 21 )
6X-RAY DIFFRACTION6chain 'C' and (resid 22 through 1773 )
7X-RAY DIFFRACTION7chain 'D' and (resid 4 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 22 through 1772 )

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