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- PDB-5v6e: Crystal structure of Myosin VI in complex with GH2 domain of GIPC1 -

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Basic information

Entry
Database: PDB / ID: 5v6e
TitleCrystal structure of Myosin VI in complex with GH2 domain of GIPC1
Components
  • PDZ domain-containing protein GIPC1
  • Unconventional myosin-VI
KeywordsPROTEIN BINDING / helical bundle
Function / homology
Function and homology information


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / regulation of secretion / Trafficking of AMPA receptors ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / RHOBTB1 GTPase cycle / presynaptic endocytic zone / RHOU GTPase cycle / RHOBTB2 GTPase cycle / Gap junction degradation / cochlear hair cell ribbon synapse / regulation of secretion / Trafficking of AMPA receptors / cellular response to electrical stimulus / positive regulation of melanin biosynthetic process / postsynaptic neurotransmitter receptor internalization / inner ear auditory receptor cell differentiation / postsynaptic actin cytoskeleton / vesicle membrane / glutamate secretion / vesicle transport along actin filament / cellular response to interleukin-7 / myosin complex / clathrin-coated vesicle / microfilament motor activity / inner ear morphogenesis / myosin binding / dendrite development / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of cytokinesis / filamentous actin / inner ear development / microvillus / brush border / endocytic vesicle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage response, signal transduction by p53 class mediator / protein targeting / endothelial cell migration / clathrin-coated pit / ruffle / synapse assembly / presynaptic modulation of chemical synaptic transmission / GTPase activator activity / dendritic shaft / locomotory behavior / filopodium / actin filament organization / PDZ domain binding / sensory perception of sound / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / regulation of protein stability / ruffle membrane / endocytosis / actin filament binding / synaptic vesicle / actin cytoskeleton / protein transport / presynapse / apical part of cell / actin binding / cell cortex / chemical synaptic transmission / cytoplasmic vesicle / postsynapse / nuclear membrane / dendritic spine / postsynaptic density / calmodulin binding / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDZ domain-containing protein GIPC1/2/3 / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain ...PDZ domain-containing protein GIPC1/2/3 / : / Myosin VI, lever arm / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding 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. / Kinesin motor domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-VI / PDZ domain-containing protein GIPC1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.506 Å
AuthorsShang, G. / Zhang, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088197 United States
Welch FoundationI-1702 United States
CitationJournal: Elife / Year: 2017
Title: Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex.
Authors: Shang, G. / Brautigam, C.A. / Chen, R. / Lu, D. / Torres-Vazquez, J. / Zhang, X.
History
DepositionMar 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: 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

Downloads & links

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Assembly

Deposited unit
A: PDZ domain-containing protein GIPC1
B: Unconventional myosin-VI
C: PDZ domain-containing protein GIPC1
D: Unconventional myosin-VI
E: PDZ domain-containing protein GIPC1
F: Unconventional myosin-VI
G: PDZ domain-containing protein GIPC1
H: Unconventional myosin-VI
I: PDZ domain-containing protein GIPC1
J: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)73,74810
Polymers73,74810
Non-polymers00
Water0
1
A: PDZ domain-containing protein GIPC1
B: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)14,7502
Polymers14,7502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PDZ domain-containing protein GIPC1
D: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)14,7502
Polymers14,7502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: PDZ domain-containing protein GIPC1
F: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)14,7502
Polymers14,7502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: PDZ domain-containing protein GIPC1
H: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)14,7502
Polymers14,7502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: PDZ domain-containing protein GIPC1
J: Unconventional myosin-VI


Theoretical massNumber of molelcules
Total (without water)14,7502
Polymers14,7502
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.979, 164.096, 171.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
PDZ domain-containing protein GIPC1 / GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / ...GAIP C-terminus-interacting protein / RGS-GAIP-interacting protein / RGS19-interacting protein 1 / SemaF cytoplasmic domain-associated protein 1 / SEMCAP-1 / Synectin


Mass: 8962.971 Da / Num. of mol.: 5 / Fragment: UNP residues 258-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gipc1, Gipc, Rgs19ip1, Semcap1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0G0
#2: Protein/peptide
Unconventional myosin-VI / / Unconventional myosin-6


Mass: 5786.563 Da / Num. of mol.: 5 / Fragment: UNP residues 1055-1099
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo6, Sv / Production host: Escherichia coli (E. coli) / References: UniProt: Q64331

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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: 5.49 Å3/Da / Density % sol: 77.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.0 and 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 20339 / % possible obs: 97 % / Redundancy: 6.1 % / Rpim(I) all: 0.074 / Net I/σ(I): 10.3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6 % / Rpim(I) all: 0.493 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V6H

5v6h


Resolution: 3.506→47.082 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1873 10.01 %
Rwork0.1865 --
obs0.1918 18709 90.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.506→47.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 0 0 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074952
X-RAY DIFFRACTIONf_angle_d0.8236661
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571834
X-RAY DIFFRACTIONf_chiral_restr0.031700
X-RAY DIFFRACTIONf_plane_restr0.003865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5065-3.60130.3227530.2678569X-RAY DIFFRACTION40
3.6013-3.70720.31591110.2468909X-RAY DIFFRACTION65
3.7072-3.82680.3031450.22051262X-RAY DIFFRACTION89
3.8268-3.96350.24031510.21361356X-RAY DIFFRACTION96
3.9635-4.12210.25711520.19681413X-RAY DIFFRACTION98
4.1221-4.30960.25641530.18861389X-RAY DIFFRACTION99
4.3096-4.53660.23591610.17231415X-RAY DIFFRACTION99
4.5366-4.82060.19261470.16941398X-RAY DIFFRACTION99
4.8206-5.19240.20531640.17781412X-RAY DIFFRACTION99
5.1924-5.71410.23151580.17761423X-RAY DIFFRACTION98
5.7141-6.53910.26641570.19711407X-RAY DIFFRACTION98
6.5391-8.23140.22391640.17111426X-RAY DIFFRACTION97
8.2314-47.08640.20861570.15611457X-RAY DIFFRACTION95
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)
11.56640.88990.76790.95420.51850.79780.3233-0.6118-0.2720.3247-0.1748-0.0560.0889-0.0230.04140.1972-0.2373-0.0810.52830.00380.1747-24.1362-93.335119.5521
24.5659-0.63851.41634.2671-0.22474.61780.11140.2979-0.1917-0.1979-0.0158-0.236-0.0690.2969-0.04930.055-0.01-0.0070.1732-0.11120.0942-31.7238-93.5571.0837
32.96241.21021.36061.49110.86452.22170.3683-0.2633-0.51320.1019-0.0640.09480.3867-0.14320.03590.1925-0.0547-0.18860.2888-0.20330.5882-46.1545-103.64960.8809
43.53470.6947-0.2753.730.85155.2028-0.08510.5681-0.6841-0.68620.2883-0.35490.20720.3588-0.18980.6974-0.0735-0.24020.5738-0.31290.6589-41.0226-110.6569-17.1556
50.2942-0.2520.11510.5268-0.37290.2897-0.2133-0.12810.2797-0.025-0.04670.0531-0.3271-0.04980.11370.5432-0.2997-0.0970.6081-0.32380.4395-4.9084-71.708624.7747
62.3585-0.5301-0.86980.83210.83551.17670.2154-0.47760.5460.1784-0.46130.6242-0.1051-0.60350.37420.361-0.11830.07990.7705-0.47890.7024-23.5804-76.013519.3732
72.80791.27881.90343.15281.33442.3699-0.36150.24550.3641-0.68870.03930.1365-0.8695-0.03330.10881.2604-0.1681-0.16910.9845-0.59121.04491.3216-43.772134.6077
82.02731.12020.34333.93080.5122.0789-0.1181-0.36230.18650.3691-0.44010.7995-0.2471-0.70170.49890.7285-0.29920.06061.2457-0.65161.067-10.8629-59.576535.7613
90.02190.02080.00940.0250.00980.0038-0.00530.01280.0022-0.04230.01040.01410.0133-0.01860.20650.2543-0.0078-0.20920.2253-0.22930.26531.9259-26.005859.1764
100.02350.0222-0.00730.02270.00570.0553-0.03090.0126-0.0085-0.0119-0.01420.03490.0345-0.0605-0.08750.82-0.0902-0.1380.6523-0.41980.67812.6481-44.50852.0284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J

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