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- PDB-4p7h: Structure of Human beta-Cardiac Myosin Motor Domain::GFP chimera -

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Basic information

Entry
Database: PDB / ID: 4p7h
TitleStructure of Human beta-Cardiac Myosin Motor Domain::GFP chimera
ComponentsMyosin-7,Green fluorescent protein
KeywordsMotor/Fluorescent Protein / Cardiac / Motor / 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 / 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 ...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 / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / bioluminescence / muscle contraction / generation of precursor metabolites and energy / Z disc / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) ...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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-7 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWinkelmann, D.A. / Miller, M.T. / Stock, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association10GRNT4300022 United States
Citation
Journal: Mol. Biol. Cell / Year: 2011
Title: Structure of Human beta-Cardiac Myosin Motor Domain at 3.2 A
Authors: Winkelmann, D.A. / Miller, M.T. / Stock, A.M. / Liu, L.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Folding of the striated muscle myosin motor domain.
Authors: Chow, D. / Srikakulam, R. / Chen, Y. / Winkelmann, D.A.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 2.0Oct 4, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy
Category: citation / entity_poly ...citation / entity_poly / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Sep 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)233,1294
Polymers232,9372
Non-polymers1922
Water905
1
A: Myosin-7,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5652
Polymers116,4691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myosin-7,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5652
Polymers116,4691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 97.730, 118.610
Angle α, β, γ (deg.)71.06, 82.67, 75.08
Int Tables number1
Space group name H-MP1

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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: 116468.672 Da / Num. of mol.: 2
Fragment: UNP P12883 residues 1-787,UNP P42212 residues 5-238
Mutation: Q80R, K101N, V163A, I167T, S175G, D190N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Tissue: muscleSkeletal muscle / Gene: MYH7, MYHCB, GFP / Organ: heart / Cell (production host): myoblast / Cell line (production host): C2C12 / Organ (production host): skeletal muscle / Production host: Mus (mice) / Tissue (production host): muscle / References: UniProt: P12883, UniProt: P42212
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe mutations in GFP were engineered to enhance folding

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 % / Description: small orthorhombic crystals with green tint
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% Tacsimate, pH 6.0, 10% glycerol, 14-15% PEG 3350, 0.2 mM MgCL2, and 5 mM TCEP
PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 25, 2011 / Details: Varimax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 3.2→39.56 Å / Num. obs: 36487 / % possible obs: 90.4 % / Redundancy: 6.7 % / Net I/σ(I): 8.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.8 / % possible all: 81.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2MYS, 2QLE

2mys

2qle


Resolution: 3.2→37.939 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 1999 5.48 %random selection
Rwork0.2263 ---
obs0.2294 36486 90.4 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→37.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15444 0 10 5 15459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215786
X-RAY DIFFRACTIONf_angle_d0.52421286
X-RAY DIFFRACTIONf_dihedral_angle_d10.0025891
X-RAY DIFFRACTIONf_chiral_restr0.022308
X-RAY DIFFRACTIONf_plane_restr0.0022754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.37561280.31122216X-RAY DIFFRACTION81
3.28-3.36860.36581280.3222206X-RAY DIFFRACTION82
3.3686-3.46770.36411350.30262306X-RAY DIFFRACTION84
3.4677-3.57950.35631340.28062339X-RAY DIFFRACTION86
3.5795-3.70740.33791400.27082399X-RAY DIFFRACTION87
3.7074-3.85570.28591410.25522444X-RAY DIFFRACTION91
3.8557-4.0310.30641480.24182529X-RAY DIFFRACTION93
4.031-4.24320.29871490.21732584X-RAY DIFFRACTION94
4.2432-4.50870.25581480.20082554X-RAY DIFFRACTION94
4.5087-4.85620.25831490.19412556X-RAY DIFFRACTION94
4.8562-5.34360.23531500.19222591X-RAY DIFFRACTION95
5.3436-6.11410.27751480.21812576X-RAY DIFFRACTION95
6.1141-7.69260.27231510.22212587X-RAY DIFFRACTION95
7.6926-37.94130.21231500.16032600X-RAY DIFFRACTION95

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