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- PDB-5wjb: Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 5wjb
TitleCrystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Gp7
ComponentsCapsid assembly scaffolding protein,Myosin-7
KeywordsActin/DNA Binding Protein / Myosin / Gp7 / Coiled-Coil / Actin-DNA Binding Protein complex
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 / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development ...viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / 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 / virion assembly / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / 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. / 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 / 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: 2.905 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 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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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)63,6304
Polymers63,6304
Non-polymers00
Water23413
1
A: Capsid assembly scaffolding protein,Myosin-7
B: Capsid assembly scaffolding protein,Myosin-7


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-63 kcal/mol
Surface area15550 Å2
MethodPISA
2
C: Capsid assembly scaffolding protein,Myosin-7
D: Capsid assembly scaffolding protein,Myosin-7


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-63 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.456, 93.706, 234.096
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
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: 15907.618 Da / Num. of mol.: 4
Fragment: UNP P13848 residues 2-47, UNP P12833 residues 1733-1797
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) / Strain (production host): CodonPlus / References: UniProt: P13848, UniProt: P12883
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.4 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% (w/v) methyl-ether PEG 2K, 1.5%(w/v) myo-inositol, 100 mM HEPES pH 7.5, 50 mM magnesium chloride

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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: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 13797 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 19.296
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 688 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO4

1no4


Resolution: 2.905→49.638 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.35
RfactorNum. reflection% reflection
Rfree0.2997 684 5 %
Rwork0.2489 --
obs0.2514 13673 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.905→49.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 0 13 3782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033805
X-RAY DIFFRACTIONf_angle_d0.5835100
X-RAY DIFFRACTIONf_dihedral_angle_d20.6071528
X-RAY DIFFRACTIONf_chiral_restr0.032567
X-RAY DIFFRACTIONf_plane_restr0.003682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9052-3.12950.33241310.30612503X-RAY DIFFRACTION99
3.1295-3.44430.31871350.28442544X-RAY DIFFRACTION100
3.4443-3.94250.29081360.25552573X-RAY DIFFRACTION100
3.9425-4.96650.26711360.21972604X-RAY DIFFRACTION100
4.9665-49.64550.31731460.23252765X-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)
17.6112-2.14192.73086.21571.09117.81860.0599-1.0734-0.87130.5081-0.6038-0.03381.2356-0.02690.15890.2908-0.1766-0.04880.58970.02260.362316.762513.337945.9139
21.2030.82062.69320.28481.64253.9391-0.0573-0.20560.081-0.0247-0.16740.08670.1726-0.05820.2840.4718-0.0392-0.05750.719-0.00180.3978-1.022810.5549-8.5874
31.55931.06771.92023.0244-0.02827.97920.0145-0.64651.41770.0093-0.45790.40030.2058-0.44780.46530.3013-0.02030.02690.529-0.19780.699713.301627.188140.0536
40.22690.53922.1560.23731.77788.8682-0.0472-0.10110.08690.0525-0.18960.02010.3459-0.11960.17760.430.0538-0.06670.7846-0.07160.3912-1.40910.5302-7.2193
57.6226-3.26291.32154.8791-2.5617.22440.1546-1.3116-0.9161-0.0530.0502-0.31660.15720.5821-0.23290.28-0.1293-0.0460.56060.04210.34596.9881-33.496946.6729
61.34631.00563.57570.29522.47978.11140.0049-0.36450.1560.0218-0.34370.03660.2939-0.53480.30750.5322-0.0881-0.10590.66990.01540.4325-12.5528-36.513-9.3837
74.50592.75442.20663.5042.65922.1654-0.2691-0.09570.6071-0.08610.06510.12140.2876-0.00620.30380.25050.02280.04080.52810.00990.53693.1073-20.231640.5691
81.79311.30275.0694-0.00292.70332.01210.1641-0.03580.08630.025-0.2005-0.00990.65770.6664-0.58020.6987-0.0408-0.1550.9486-0.04960.4329-12.323-36.4405-6.9853
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 1797 )
3X-RAY DIFFRACTION3chain 'B' and (resid -8 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 1797 )
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 23 )
6X-RAY DIFFRACTION6chain 'C' and (resid 24 through 1797 )
7X-RAY DIFFRACTION7chain 'D' and (resid -7 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 22 through 1797 )

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