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- PDB-4pa0: Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin... -

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Basic information

Entry
Database: PDB / ID: 4pa0
TitleOmecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin Motor Domain
ComponentsMyosin-7,Green fluorescent protein
KeywordsMotor/Fluorescent Protein / Cardiac / Myosin / Motor / omecamtiv mercarbil / Motor-Fluorescent Protein complex
Function / homology
Function and homology information


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 ...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 / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cardiac muscle contraction / stress fiber / muscle contraction / regulation of heart rate / bioluminescence / sarcomere / generation of precursor metabolites and energy / Z disc / actin filament binding / calmodulin binding / ATP binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-2OW / Myosin-7 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWinkelmann, D.A. / Miller, M.T. / Stock, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association10GRNT4300022 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for drug-induced allosteric changes to human beta-cardiac myosin motor activity.
Authors: Winkelmann, D.A. / Forgacs, E. / Miller, M.T. / Stock, A.M.
History
DepositionApr 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-7,Green fluorescent protein
B: Myosin-7,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,2997
Polymers233,2202
Non-polymers1,0795
Water5,513306
1
A: Myosin-7,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0112
Polymers116,6101
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-7,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2885
Polymers116,6101
Non-polymers6784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.167, 88.924, 137.786
Angle α, β, γ (deg.)90.00, 93.92, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer in solution based on gel filtration

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Components

#1: Protein Myosin-7,Green fluorescent protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 116609.812 Da / Num. of mol.: 2
Fragment: UNP P12883 residues 1-787, UNP P42212 residues 5-234
Mutation: Q80R, V163A, I167T, S175G, D190N
Source method: isolated from a genetically manipulated source
Details: cloned cDNA
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Tissue: muscle / Cell: cardiomyocyte / Gene: MYH7, MYHCB, GFP / Organ: Heart
Details (production host): replication defective adenovirus infection
Cell (production host): myoblast / Cell line (production host): C2C12 cells / Organ (production host): skeletal muscle / Production host: Mus (mice) / Tissue (production host): muscle / References: UniProt: P12883, UniProt: P42212
#2: Chemical ChemComp-2OW / methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate / omecamtiv mercarbil


Mass: 401.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN5O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsYKDHD are a minimal Flag epitope tag engineered into the sequence to facilitate purification by the author

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 % / Description: small orthorhombic crystals, green in color
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Tacsimate, pH 6.0, PEG 3350, glycerol, MgCL2, TCEP and ligand, omecamptiv mercarbil
PH range: 5.8-6.4 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: crystals cryopreserved in mother liquor
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2014
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→46.042 Å / Num. obs: 106961 / % possible obs: 93.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.499 / Mean I/σ(I) obs: 0.8 / % possible all: 84

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7H

4p7h


Resolution: 2.25→45.961 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5383 5.03 %Xtriage
Rwork0.2012 ---
obs0.2034 106961 93.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→45.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14595 0 76 306 14977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114988
X-RAY DIFFRACTIONf_angle_d1.32720283
X-RAY DIFFRACTIONf_dihedral_angle_d15.4195364
X-RAY DIFFRACTIONf_chiral_restr0.0532235
X-RAY DIFFRACTIONf_plane_restr0.0072633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.36551560.32633043X-RAY DIFFRACTION83
2.2756-2.30240.36861720.31592985X-RAY DIFFRACTION84
2.3024-2.33040.35721510.31983078X-RAY DIFFRACTION84
2.3304-2.35990.36091640.30863019X-RAY DIFFRACTION84
2.3599-2.3910.33441570.30753091X-RAY DIFFRACTION85
2.391-2.42370.36461890.29753072X-RAY DIFFRACTION86
2.4237-2.45840.34691660.28733139X-RAY DIFFRACTION86
2.4584-2.4950.29841700.28683151X-RAY DIFFRACTION87
2.495-2.5340.32371630.27663160X-RAY DIFFRACTION88
2.534-2.57560.33731920.26443225X-RAY DIFFRACTION90
2.5756-2.620.27781640.25053331X-RAY DIFFRACTION92
2.62-2.66760.32782080.24893299X-RAY DIFFRACTION93
2.6676-2.71890.28941780.23993379X-RAY DIFFRACTION93
2.7189-2.77440.24581920.22993434X-RAY DIFFRACTION94
2.7744-2.83470.28531890.22323377X-RAY DIFFRACTION94
2.8347-2.90070.28691890.22133431X-RAY DIFFRACTION95
2.9007-2.97320.28141770.21643503X-RAY DIFFRACTION96
2.9732-3.05360.30021730.21833469X-RAY DIFFRACTION95
3.0536-3.14340.24251900.20683451X-RAY DIFFRACTION96
3.1434-3.24480.23851720.19653509X-RAY DIFFRACTION96
3.2448-3.36080.24731870.19463551X-RAY DIFFRACTION97
3.3608-3.49530.23141830.18243534X-RAY DIFFRACTION98
3.4953-3.65430.21051700.17753622X-RAY DIFFRACTION99
3.6543-3.84690.19341760.16593670X-RAY DIFFRACTION100
3.8469-4.08770.19632190.16683582X-RAY DIFFRACTION100
4.0877-4.40310.20141630.15373691X-RAY DIFFRACTION100
4.4031-4.84580.18682030.14993642X-RAY DIFFRACTION100
4.8458-5.5460.21261710.16753697X-RAY DIFFRACTION100
5.546-6.98340.22961960.19963680X-RAY DIFFRACTION100
6.9834-45.97080.21172030.1613763X-RAY DIFFRACTION100

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