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- PDB-4xa1: Crystal Structure of the coiled-coil surrounding Skip 1 of MYH7 -

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Basic information

Entry
Database: PDB / ID: 4xa1
TitleCrystal Structure of the coiled-coil surrounding Skip 1 of MYH7
ComponentsGp7-MYH7(1173-1238)-EB1 chimera protein
KeywordsMOTOR PROTEIN / Myosin / coiled coil / skip residue / fusion / Gp7 / EB1 / MYH7 / Cardiac
Function / homology
Function and homology information


viral scaffold / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / muscle myosin complex ...viral scaffold / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / muscle myosin complex / cell projection membrane / mitotic spindle microtubule / regulation of the force of heart contraction / attachment of mitotic spindle microtubules to kinetochore / transition between fast and slow fiber / myosin filament / microtubule bundle formation / microtubule plus-end binding / adult heart development / non-motile cilium assembly / cardiac muscle hypertrophy in response to stress / muscle filament sliding / protein localization to centrosome / myosin complex / myosin II complex / ventricular cardiac muscle tissue morphogenesis / virion assembly / microfilament motor activity / mitotic spindle pole / negative regulation of microtubule polymerization / spindle midzone / myofibril / microtubule polymerization / microtubule organizing center / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / spindle assembly / cytoplasmic microtubule / cardiac muscle contraction / stress fiber / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / muscle contraction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / regulation of heart rate / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / sarcomere / RHO GTPases Activate Formins / Z disc / actin filament binding / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / microtubule / calmodulin binding / ciliary basal body / cadherin binding / cell division / focal adhesion / centrosome / Golgi apparatus / DNA binding / RNA binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / DNA repair protein XRCC4-like, C-terminal / Myosin tail ...Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / 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. / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-7 / Capsid assembly scaffolding protein / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTaylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinz, N.T. / Qiang, C. / Leinwand, L.A. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL111237 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly.
Authors: Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinze, N.T. / Cui, Q. / Leinwand, L.A. / Rayment, I.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gp7-MYH7(1173-1238)-EB1 chimera protein
B: Gp7-MYH7(1173-1238)-EB1 chimera protein
C: Gp7-MYH7(1173-1238)-EB1 chimera protein
D: Gp7-MYH7(1173-1238)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)73,7864
Polymers73,7864
Non-polymers00
Water63135
1
A: Gp7-MYH7(1173-1238)-EB1 chimera protein
B: Gp7-MYH7(1173-1238)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)36,8932
Polymers36,8932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-73 kcal/mol
Surface area19600 Å2
MethodPISA
2
C: Gp7-MYH7(1173-1238)-EB1 chimera protein
D: Gp7-MYH7(1173-1238)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)36,8932
Polymers36,8932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-65 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.260, 59.321, 67.721
Angle α, β, γ (deg.)96.05, 110.01, 92.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Gp7-MYH7(1173-1238)-EB1 chimera protein / chimera protein of Head morphogenesis protein / Myosin-7 and Microtubule-associated protein RP/EB ...chimera protein of Head morphogenesis protein / Myosin-7 and Microtubule-associated protein RP/EB family member 1


Mass: 18446.553 Da / Num. of mol.: 4
Fragment: UNP P13848 residues 1-49,UNP Q12883 residues 1173-1238,UNP Q15691 residues 211-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pET28 / Gene: MYH7, MYHCB, MAPRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13848, UniProt: P12883, UniProt: Q15691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.85 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20% (w/v) polyethylene glycol methyl ether 2000, 20 mM SrCl2, 100 mM HEPES pH 7.6, 5% pentaerythritol ethoxylate (17/8 PO/OH) 797, 0.5% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13198 / % possible obs: 97 % / Redundancy: 2 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.03 / Net I/av σ(I): 15.5 / Net I/σ(I): 12.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 7.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N04, 1YIB

1n04

1yib


Resolution: 3.2→34.861 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 675 5.12 %Random Selection
Rwork0.2343 ---
obs0.2371 13176 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 0 35 4626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134638
X-RAY DIFFRACTIONf_angle_d1.6056219
X-RAY DIFFRACTIONf_dihedral_angle_d17.9921853
X-RAY DIFFRACTIONf_chiral_restr0.087691
X-RAY DIFFRACTIONf_plane_restr0.005829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1944-3.44080.35621470.27282480X-RAY DIFFRACTION98
3.4408-3.78670.31931140.24042581X-RAY DIFFRACTION99
3.7867-4.33380.24851350.20192509X-RAY DIFFRACTION99
4.3338-5.45670.27431380.21742518X-RAY DIFFRACTION98
5.4567-34.86270.27641410.2562413X-RAY DIFFRACTION95

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