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- PDB-5wlq: Crystal Structure of Amino Acids 1677-1755 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 5wlq
TitleCrystal Structure of Amino Acids 1677-1755 of Human Beta Cardiac Myosin Fused to Gp7 and Eb1
ComponentsCapsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / Myosin / Gp7 / Coiled-Coil / Eb1
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 / microfilament motor activity / virion assembly / mitotic spindle pole / spindle midzone / negative regulation of microtubule polymerization / 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 / cytoplasmic microtubule / cardiac muscle contraction / stress fiber / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Mitotic Prometaphase / Recruitment of NuMA to mitotic centrosomes / EML4 and NUDC in mitotic spindle formation / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / regulation of heart rate / muscle contraction / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / sarcomere / RHO GTPases Activate Formins / Z disc / The role of GTSE1 in G2/M progression after G2 checkpoint / actin filament binding / Separation of Sister Chromatids / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / 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 / cytosol / cytoplasm
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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
trimethylamine oxide / 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: 3.104 Å
AuthorsAndreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111237 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod.
Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I.
History
DepositionJul 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Capsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1786
Polymers20,7821
Non-polymers3975
Water1448
1
A: Capsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1
hetero molecules

A: Capsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,35712
Polymers41,5642
Non-polymers79310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5630 Å2
ΔGint-59 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.756, 141.756, 87.381
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Capsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1 / Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Myosin heavy ...Gene product 7 / gp7 / Head morphogenesis protein / Protein p7 / Scaffold protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 20781.934 Da / Num. of mol.: 1
Fragment: UNP P13848 residues 2-48 UNP Q15691 residues 208-256, UNP P12883 residues 1677-1755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Gene: MYH7, MYHCB, MAPRE1 / Production host: Escherichia coli (E. coli)
References: UniProt: P13848, UniProt: P12883, UniProt: Q15691
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 6.3 Å3/Da / Density % sol: 80.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6 M Ammonium Aulfate, 500 mM Trimethyl Ammonium N-Oxide, 100 mM Bis-tris Propane pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 9815 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 24.2
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 478 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 3.104→41.161 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.75
RfactorNum. reflection% reflection
Rfree0.2364 462 5 %
Rwork0.2224 --
obs0.2231 9244 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.104→41.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 25 8 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003875
X-RAY DIFFRACTIONf_angle_d0.4861180
X-RAY DIFFRACTIONf_dihedral_angle_d12.23549
X-RAY DIFFRACTIONf_chiral_restr0.032132
X-RAY DIFFRACTIONf_plane_restr0.002154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1036-3.55250.26811320.24542501X-RAY DIFFRACTION83
3.5525-4.47490.20271600.20763050X-RAY DIFFRACTION100
4.4749-41.16510.25221700.22533231X-RAY DIFFRACTION100
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)
17.21020.8689-0.58788.0127-0.16973.07510.297-0.1053-0.89110.1945-0.1652-0.14060.709-0.644-0.12490.4669-0.1886-0.04950.2519-0.00250.1879-5.222570.55418.6576
25.28543.2507-0.92371.9253-0.57470.1467-0.17860.33720.1211-0.11380.22940.11040.0361-0.12910.02780.2888-0.33270.01540.5664-0.01770.2743-51.045253.91976.0724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 1731 )

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