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- PDB-9f6c: Cardiac myosin motor domain in the pre-powerstroke state co-cryst... -

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Basic information

Entry
Database: PDB / ID: 9f6c
TitleCardiac myosin motor domain in the pre-powerstroke state co-crystallized with the inhibitor aficamten
ComponentsMyosin-7
KeywordsMOTOR PROTEIN / cardiac myosin / modulator / cardiomyopathy / force production
Function / homology
Function and homology information


myosin filament / adult heart development / muscle filament sliding / myosin II complex / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding / calmodulin binding ...myosin filament / adult heart development / muscle filament sliding / myosin II complex / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding / calmodulin binding / ATP binding / cytoplasm
Similarity search - Function
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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin-7
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsRobert-Paganin, J. / Hartman, J.J. / Morgan, B.P. / Malik, F.I. / Houdusse, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Cardiovasc Res / Year: 2024
Title: Aficamten is a small-molecule cardiac myosin inhibitor designed to treat hypertrophic cardiomyopathy.
Authors: Hartman, J.J. / Hwee, D.T. / Robert-Paganin, J. / Chuang, C. / Chin, E.R. / Edell, S. / Lee, K.H. / Madhvani, R. / Paliwal, P. / Pernier, J. / Sarkar, S.S. / Schaletzky, J. / Schauer, K. / ...Authors: Hartman, J.J. / Hwee, D.T. / Robert-Paganin, J. / Chuang, C. / Chin, E.R. / Edell, S. / Lee, K.H. / Madhvani, R. / Paliwal, P. / Pernier, J. / Sarkar, S.S. / Schaletzky, J. / Schauer, K. / Taheri, K.D. / Wang, J. / Wehri, E. / Wu, Y. / Houdusse, A. / Morgan, B.P. / Malik, F.I.
History
DepositionMay 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-7
B: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,53411
Polymers178,6302
Non-polymers1,9049
Water5,945330
1
A: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3156
Polymers89,3151
Non-polymers1,0005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2195
Polymers89,3151
Non-polymers9044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.424, 128.326, 103.530
Angle α, β, γ (deg.)90.000, 91.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myosin-7 / 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: 89315.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MYH7 / Production host: Bos taurus (domestic cattle) / References: UniProt: Q9BE39

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Non-polymers , 6 types, 339 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-6I6 / aficamten / ~{N}-[(1~{R})-5-(5-ethyl-1,2,4-oxadiazol-3-yl)-2,3-dihydro-1~{H}-inden-1-yl]-1-methyl-pyrazole-4-carboxamide


Mass: 337.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 23% PEG3350; 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 7.9

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.33→103.496 Å / Num. obs: 51951 / % possible obs: 93.8 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.4
Reflection shellResolution: 2.33→2.59 Å / Num. unique obs: 2599 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→46.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.907 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.795 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2562 4.93 %RANDOM
Rwork0.205 ---
obs0.207 51942 67.2 %-
Displacement parametersBiso max: 198.01 Å2 / Biso mean: 74.86 Å2 / Biso min: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.0892 Å20 Å2-3.8411 Å2
2---4.8846 Å20 Å2
3---5.9738 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.33→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11465 0 121 330 11916
Biso mean--57.06 63.56 -
Num. residues----1423
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4237SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes322HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1746HARMONIC5
X-RAY DIFFRACTIONt_it11860HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13446SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11860HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16011HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion19.85
LS refinement shellResolution: 2.33→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 8 6.3 %
Rwork0.21 119 -
all0.214 127 -
obs--2.21 %
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)
10.88160.503-0.49751.4894-0.96161.342-0.0314-0.02470.03150.0130.04790.04280.11820.1242-0.0165-0.1755-0.0112-0.0701-0.1959-0.0435-0.062111.22968.346143.5798
21.1976-0.97830.94913.0527-2.0762.6345-0.0653-0.0331-0.0055-0.1749-0.1088-0.1362-0.00640.21470.1741-0.292-0.0354-0.0325-0.2992-0.0285-0.172478.4311-12.32127.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A33 - 1001
2X-RAY DIFFRACTION2{ B|* }B33 - 781

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