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- PDB-6fsa: Beta-Cardiac myosin post-rigor -

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Basic information

Entry
Database: PDB / ID: 6fsa
TitleBeta-Cardiac myosin post-rigor
Components
  • Myosin light chain 3
  • Myosin-7
KeywordsMOTOR PROTEIN / myosin / hypertrophic cardiomyopathy
Function / homology
Function and homology information


muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding ...muscle filament sliding / myosin filament / myosin II complex / adult heart development / sarcomere organization / microfilament motor activity / myofibril / cardiac muscle contraction / sarcomere / actin filament binding / calmodulin binding / calcium ion 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. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FORMIC ACID / Myosin light chain 3 / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsRobert-Paganin, J. / Auguin, D. / Houdusse, A.
Funding support France, 3items
OrganizationGrant numberCountry
AFM (Association Francaise contre les Myopathies)18423 France
AFM (Association Francaise contre les Myopathies)17235 France
FRM (Fondation Pour la recherche medicale en France)DBI20141231319 France
CitationJournal: Nat Commun / Year: 2018
Title: Hypertrophic cardiomyopathy disease results from disparate impairments of cardiac myosin function and auto-inhibition.
Authors: Robert-Paganin, J. / Auguin, D. / Houdusse, A.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation_wavelength / Item: _citation.title
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
D: Myosin light chain 3
H: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,40615
Polymers491,1484
Non-polymers1,25711
Water13,944774
1
A: Myosin-7
D: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,1807
Polymers245,5742
Non-polymers6065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-27 kcal/mol
Surface area42990 Å2
MethodPISA
2
B: Myosin-7
H: Myosin light chain 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,2268
Polymers245,5742
Non-polymers6526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area41240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.118, 94.319, 125.411
Angle α, β, γ (deg.)104.76, 92.34, 100.06
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABDH

#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: 223606.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9BE39
#2: Protein Myosin light chain 3 / / Myosin light chain 1 / slow-twitch muscle B/ventricular isoform / MLC1SB


Mass: 21968.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P85100

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Non-polymers , 5 types, 785 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / 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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12.5% PEG mix MMW (2k, 3350, 4k, 5k MME), 10% glycerol, 7.5% Sodium Tacsimate pH 6.0, 0.5 mM TCEP

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.33→47.97 Å / Num. obs: 100862 / % possible obs: 98.46 % / Redundancy: 3.6 % / Biso Wilson estimate: 49.36 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.1605 / Net I/σ(I): 7.76
Reflection shellResolution: 2.33→2.413 Å / Num. unique obs: 10032 / % possible all: 97.87

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7H

4p7h


Resolution: 2.33→47.97 Å / Cor.coef. Fo:Fc: 0.9326 / Cor.coef. Fo:Fc free: 0.9081 / SU R Cruickshank DPI: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.273 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 4907 4.87 %RANDOM
Rwork0.1895 ---
obs0.1913 100842 98.37 %-
Displacement parametersBiso mean: 67.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.5664 Å26.0433 Å24.3181 Å2
2--4.4779 Å2-2.1449 Å2
3----3.9114 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: 1 / Resolution: 2.33→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14633 0 79 774 15486
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115038HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1220298HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5333SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes414HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2184HARMONIC5
X-RAY DIFFRACTIONt_it15038HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion19.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1959SEMIHARMONIC5
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_contact17579SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2571 401 5.37 %
Rwork0.2244 7060 -
all0.2262 7461 -
obs--96.23 %

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