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- PDB-4xa6: Crystal Structure of the coiled-coil surrounding Skip 4 of MYH7 -

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Basic information

Entry
Database: PDB / ID: 4xa6
TitleCrystal Structure of the coiled-coil surrounding Skip 4 of MYH7
ComponentsGp7-MYH7(1777-1855)-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 / muscle filament sliding / mitotic spindle microtubule / cell projection membrane / regulation of the force of heart contraction / transition between fast and slow fiber / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / myosin filament / microtubule bundle formation / non-motile cilium assembly / adult heart development / cardiac muscle hypertrophy in response to stress / protein localization to centrosome / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microtubule organizing center / microfilament motor activity / negative regulation of microtubule polymerization / virion assembly / mitotic spindle pole / myofibril / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / skeletal muscle contraction / spindle midzone / regulation of microtubule polymerization or depolymerization / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ATP metabolic process / striated muscle contraction / stress fiber / cardiac muscle contraction / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of microtubule polymerization / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of heart rate / sarcomere / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / Z disc / Separation of Sister Chromatids / actin filament binding / cell migration / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / protein localization / microtubule / calmodulin binding / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / 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 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: 3.42 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 ...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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6Nov 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: Gp7-MYH7(1777-1855)-EB1 chimera protein
B: Gp7-MYH7(1777-1855)-EB1 chimera protein
C: Gp7-MYH7(1777-1855)-EB1 chimera protein
D: Gp7-MYH7(1777-1855)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)84,8864
Polymers84,8864
Non-polymers00
Water00
1
A: Gp7-MYH7(1777-1855)-EB1 chimera protein
B: Gp7-MYH7(1777-1855)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)42,4432
Polymers42,4432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-81 kcal/mol
Surface area23100 Å2
MethodPISA
2
C: Gp7-MYH7(1777-1855)-EB1 chimera protein
D: Gp7-MYH7(1777-1855)-EB1 chimera protein


Theoretical massNumber of molelcules
Total (without water)42,4432
Polymers42,4432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-58 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.546, 46.889, 169.055
Angle α, β, γ (deg.)90.00, 94.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Gp7-MYH7(1777-1855)-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: 21221.461 Da / Num. of mol.: 4
Fragment: UNP P13848 residues 2-50,UNP P02564 residues 1777-1855,UNP Q15691 residues 209-251
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

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% (w/v) polyethylene glycol 2000 methyl ether, 100 mM piperazine-N,N-bis(2-ethanesulfonic acid) (PIPES)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 15120 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.08 / Net I/av σ(I): 10.1 / Net I/σ(I): 14.8
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO4, 1YIB

1no4

1yib


Resolution: 3.42→43.887 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2967 675 4.48 %Random Selection
Rwork0.2392 ---
obs0.2419 15052 88.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.42→43.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 0 0 4726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064766
X-RAY DIFFRACTIONf_angle_d0.9256375
X-RAY DIFFRACTIONf_dihedral_angle_d18.311974
X-RAY DIFFRACTIONf_chiral_restr0.037667
X-RAY DIFFRACTIONf_plane_restr0.004830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4202-3.68420.3033880.26221584X-RAY DIFFRACTION50
3.6842-4.05470.31131550.23643077X-RAY DIFFRACTION96
4.0547-4.64090.29491490.22473193X-RAY DIFFRACTION100
4.6409-5.84480.28711420.25533283X-RAY DIFFRACTION100
5.8448-43.89030.28881410.23313240X-RAY DIFFRACTION97
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)
10.02430.0059-0.0180.10550.00720.1143-0.02390.0343-0.0096-0.20340.0015-0.0913-0.08830.0017-0.03980.45570.05660.0685-0.13710.1856-0.020333.6353-21.605911.0626
20.0138-0.0089-0.00470.0160.00860.0067-0.0220.0173-0.01150.004-0.06290.00490.0912-0.021-0.00880.25410.03360.15720.34120.07030.4631.5023-40.695763.1858
30.0149-0.01610.02510.0261-0.02540.03790.0613-0.1026-0.0450.02920.0484-0.15250.0559-0.0350.09910.0798-0.2563-0.16960.4457-0.00530.2992-52.148-40.812494.7085
40.2718-0.1816-0.06140.42820.09380.2435-0.2086-0.2925-0.086-0.2428-0.20550.127-0.0105-0.2458-0.6290.06320.0680.0188-0.21440.2302-0.087120.9537-31.155632.4825
50.02450.01920.00370.02210.00810.00260.0013-0.03530.01970.0057-0.01540.0087-0.0096-0.0481-0.04690.1128-0.2071-0.04780.4095-0.11870.2791-57.3676-38.937392.8673
60.03180.0226-0.01710.0128-0.00480.0268-0.0004-0.03370.00730.01860.0071-0.02950.002-0.0401-0.0020.0824-0.2621-0.00550.3542-0.09210.1823-52.7908-33.5583123.5915
70.0266-0.0392-0.03950.04990.05770.07130.099-0.0249-0.0363-0.02910.0175-0.02840.00450.00120.05420.04960.03790.06320.49760.14830.0823-24.053-17.226490.1341
80.03430.0095-0.00120.00920.0018-0.001-0.0257-0.0744-0.0067-0.02070.0082-0.0449-0.029-0.0766-0.00680.07550.21280.03680.25350.02990.116310.3929-16.546748.3385
90.0141-0.0137-0.00590.01330.00310.0060.02130.0152-0.0045-0.01170.0111-0.04670.00650.01920.0040.323-0.07580.0660.1794-0.13550.267233.0075-12.78738.4253
100.00420.0045-0.00080.0012-0.00190.00150.007-0.0086-0.0087-0.01560.00310.00360.0065-0.00270.01380.1568-0.1455-0.14730.4649-0.11880.3163-47.9152-34.0983107.4869
110.00060.0003-0.00010.00270.00150.00030.01780.0134-0.0155-0.0025-0.0085-0.01350.0180.00480.00980.05740.0099-0.07760.35030.06790.2688-25.4795-25.109788.5956
120.01960.0124-0.01140.0097-0.01050.01080.03840.0010.0054-0.01570.0224-0.0259-0.00870.0012-0.00010.34010.0651-0.05510.7010.02920.4422-2.93-20.936774.6483
130.05220.038-0.01460.1580.05190.15270.0211-0.01670.0477-0.16340.059-0.1437-0.1055-0.0061-0.02040.22850.13910.17330.31210.06190.217717.9157-9.516447.7058
140.002-0.00070.00190.0068-0.00240.00220.00280.00560.0058-0.0054-0.00620.02330.00620.00320.00350.22690.14140.00180.12090.03120.208221.1221-11.009830.5309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2:50 or 1777:1804 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1805:1837 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1839:1855 or 209:248 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3:50 or 1777:1845 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1846:1855 or 209:247 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1781:1804 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1805:1841 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1843:1855 or 209:230 )
9X-RAY DIFFRACTION9chain 'C' and (resid 231:249 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1792:1811 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1812:1833 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1834:1845 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1846:1855 or 209:236 )
14X-RAY DIFFRACTION14chain 'D' and (resid 237:248 )

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