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- PDB-5cj1: Crystal structure of the coiled coil of MYH7 residues 1526 to 157... -

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Basic information

Entry
Database: PDB / ID: 5cj1
TitleCrystal structure of the coiled coil of MYH7 residues 1526 to 1571 fused to Gp7
ComponentsGp7-MYH7-(1526-1571) chimera protein
KeywordsMOTOR PROTEIN / myosin / coiled coil / fusion
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: 2.1 Å
AuthorsTaylor, K.C. / Korkmaz, E.N. / Andreas, M.P. / Ajay, G. / Heinz, N.T. / Cui, Q. / 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: 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 1.3Dec 4, 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
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: Gp7-MYH7-(1526-1571) chimera protein
B: Gp7-MYH7-(1526-1571) chimera protein
C: Gp7-MYH7-(1526-1571) chimera protein
D: Gp7-MYH7-(1526-1571) chimera protein
E: Gp7-MYH7-(1526-1571) chimera protein
F: Gp7-MYH7-(1526-1571) chimera protein
G: Gp7-MYH7-(1526-1571) chimera protein
H: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)92,3828
Polymers92,3828
Non-polymers00
Water3,027168
1
A: Gp7-MYH7-(1526-1571) chimera protein
B: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-43 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: Gp7-MYH7-(1526-1571) chimera protein
D: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-42 kcal/mol
Surface area13470 Å2
MethodPISA
3
E: Gp7-MYH7-(1526-1571) chimera protein
F: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-43 kcal/mol
Surface area13400 Å2
MethodPISA
4
G: Gp7-MYH7-(1526-1571) chimera protein
H: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-40 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.085, 64.466, 93.594
Angle α, β, γ (deg.)70.53, 77.51, 74.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Gp7-MYH7-(1526-1571) chimera protein / Gene product 7 / Gp7 / Head morphogenesis protein / Scaffold protein / Myosin heavy chain 7 / ...Gene product 7 / Gp7 / Head morphogenesis protein / Scaffold protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 11547.798 Da / Num. of mol.: 8
Fragment: UNP P13848 residues 2-52, UNP P12833 residues 1526-1571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pET31b / Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13848, UniProt: P12883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (w/v) PEG 8000, 400 mM malonate pH 7.2, and 100 mM triethanolamine pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2014
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 67161 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.26 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 23.15 / Net I/σ(I): 15.57
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO4

1no4


Resolution: 2.1→48.679 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3282 4.89 %Random selection
Rwork0.2075 ---
obs0.2096 67072 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 168 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086415
X-RAY DIFFRACTIONf_angle_d0.8918597
X-RAY DIFFRACTIONf_dihedral_angle_d17.1792574
X-RAY DIFFRACTIONf_chiral_restr0.035942
X-RAY DIFFRACTIONf_plane_restr0.0041153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0969-2.12820.40541200.28572511X-RAY DIFFRACTION88
2.1282-2.16150.3031680.27232733X-RAY DIFFRACTION97
2.1615-2.19690.26481340.25582758X-RAY DIFFRACTION97
2.1969-2.23480.30461510.23542789X-RAY DIFFRACTION96
2.2348-2.27550.27861300.22762744X-RAY DIFFRACTION97
2.2755-2.31920.29351400.22652769X-RAY DIFFRACTION97
2.3192-2.36660.2871570.22352755X-RAY DIFFRACTION97
2.3666-2.4180.29621460.22312753X-RAY DIFFRACTION97
2.418-2.47430.28811510.22382798X-RAY DIFFRACTION97
2.4743-2.53610.30251350.22582802X-RAY DIFFRACTION98
2.5361-2.60470.30231340.22882782X-RAY DIFFRACTION98
2.6047-2.68130.29271440.24172822X-RAY DIFFRACTION98
2.6813-2.76790.28941510.24272762X-RAY DIFFRACTION98
2.7679-2.86680.28131280.26292806X-RAY DIFFRACTION98
2.8668-2.98160.3391410.25382785X-RAY DIFFRACTION98
2.9816-3.11720.29351610.25542809X-RAY DIFFRACTION98
3.1172-3.28160.26311370.24842814X-RAY DIFFRACTION98
3.2816-3.48710.26811450.21932818X-RAY DIFFRACTION98
3.4871-3.75620.21711610.19992798X-RAY DIFFRACTION98
3.7562-4.13410.23021410.17432790X-RAY DIFFRACTION98
4.1341-4.73180.171260.1532832X-RAY DIFFRACTION98
4.7318-5.95990.19411320.1572825X-RAY DIFFRACTION98
5.9599-48.69230.1711490.1442735X-RAY DIFFRACTION96
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)
15.2412-3.0708-0.46545.99580.91014.87250.0235-0.18170.65930.01820.0868-0.6559-0.3230.1215-0.09810.2691-0.03670.03460.1930.00990.2717-27.7314-5.157821.6882
27.7754-3.6014.49661.4426-2.12162.1454-0.1393-0.6618-0.23580.05640.28410.1061-0.019-0.2787-0.23890.3550.1093-0.02470.41380.01920.26047.119-30.68535.9379
38.00050.6081-1.20967.41740.09395.7410.3398-0.46260.3110.4388-0.0492-0.6334-0.29720.6819-0.24080.25170.0195-0.06980.33270.00860.2571-8.79283.8559-14.4107
42.48452.6901-4.09410.4902-1.29992.0203-0.0020.2115-0.1227-0.05210.0445-0.00310.0215-0.12430.06240.3421-0.03360.0450.48180.10650.4362-52.1805-11.0798-7.5786
58.2560.7723-0.78364.9112.21427.2060.5454-0.2026-0.0173-0.4439-0.37090.19020.4278-0.4522-0.12580.196-0.0515-0.00050.17570.02660.1652-33.6604-18.542520.4374
67.7821-4.03062.27591.6016-1.06490.3965-0.1624-0.08150.58120.06750.0075-0.2556-0.00760.02030.11980.28890.0542-0.04850.3143-0.0070.33778.5723-27.23535.5726
78.54430.72420.58196.8257-0.38735.28370.4167-1.2410.95310.6387-0.3306-0.45620.05950.3125-0.03870.3676-0.0451-0.09690.4993-0.1310.4142-22.403624.7519-5.3695
86.9291-4.66053.02552.2017-1.70190.92770.1590.56960.3149-0.005-0.282-0.19630.02670.20420.12970.39020.0879-0.11270.46410.08370.598-63.561836.5756-24.5192
97.3261-1.16592.93775.93033.67165.13940.14370.0278-0.0884-0.0179-0.62470.3453-0.3344-0.72410.36180.34040.05450.05760.3566-0.05120.2213-43.32826.443338.9863
108.63774.9682-2.56732.1744-1.28010.5613-0.13350.089-0.5825-0.04120.0053-0.2999-0.0063-0.02050.11310.3053-0.05040.05930.2697-0.00740.4365-1.453815.620823.4076
116.56720.7098-2.51143.0829-1.5326.82030.0891-0.0766-0.53170.80540.03920.24870.9017-0.333-0.06730.4681-0.04120.09050.19540.00880.3779-36.5441-6.352139.3138
127.55093.7194-4.5261.6142-2.25662.4468-0.18450.5910.1325-0.05690.30570.06840.0941-0.2631-0.14740.3453-0.09770.03970.3363-0.0360.2481-2.969519.700522.9086
136.4-2.6843-1.08468.8784-0.11833.75340.41370.4571-0.1579-0.8886-0.3619-0.31440.01410.1079-0.08570.35270.0415-0.0290.2517-0.02060.4616-23.497319.5042-18.988
147.3983-3.53953.38270.7594-1.16381.0277-0.5171-1.0305-0.20150.17830.4977-0.0449-0.1773-0.3590.15820.36130.0791-0.07550.47360.050.5278-63.747736.7993-21.9257
158.2441-0.3382-1.25293.40411.06753.81550.15240.5170.0432-0.5572-0.03160.0811-0.031-0.0626-0.19280.51150.0636-0.04360.34320.0470.2229-14.43041.5108-27.5234
168.35925.2538-3.75372.7705-2.12071.05520.1015-0.5189-0.3709-0.0213-0.3043-0.1909-0.01880.20830.19760.3545-0.10660.07320.51940.0730.489-50.4712-11.0442-4.2857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 23 )
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 1571 )
3X-RAY DIFFRACTION3chain 'F' and (resid 4 through 23 )
4X-RAY DIFFRACTION4chain 'F' and (resid 24 through 1571 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 23 )
6X-RAY DIFFRACTION6chain 'A' and (resid 24 through 1571 )
7X-RAY DIFFRACTION7chain 'H' and (resid 5 through 23 )
8X-RAY DIFFRACTION8chain 'H' and (resid 24 through 1571 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 23 )
10X-RAY DIFFRACTION10chain 'C' and (resid 24 through 1571 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 23 )
12X-RAY DIFFRACTION12chain 'D' and (resid 24 through 1571 )
13X-RAY DIFFRACTION13chain 'G' and (resid 3 through 23 )
14X-RAY DIFFRACTION14chain 'G' and (resid 24 through 1570 )
15X-RAY DIFFRACTION15chain 'E' and (resid 3 through 23 )
16X-RAY DIFFRACTION16chain 'E' and (resid 24 through 1571 )

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