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- PDB-3pvl: Structure of myosin VIIa MyTH4-FERM-SH3 in complex with the CEN1 ... -

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Basic information

Entry
Database: PDB / ID: 3pvl
TitleStructure of myosin VIIa MyTH4-FERM-SH3 in complex with the CEN1 of Sans
Components
  • Myosin VIIa isoform 1
  • Usher syndrome type-1G protein
KeywordsMOTOR PROTEIN/PROTEIN TRANSPORT / protein complex / Novel folding / protein cargo binding / cargo proteins / MOTOR PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


: / photoreceptor cell cilium / pigment granule localization / upper tip-link density / pigment granule transport / stereocilium base / The canonical retinoid cycle in rods (twilight vision) / microfilament motor activity => GO:0000146 / myosin VII complex / phagolysosome assembly ...: / photoreceptor cell cilium / pigment granule localization / upper tip-link density / pigment granule transport / stereocilium base / The canonical retinoid cycle in rods (twilight vision) / microfilament motor activity => GO:0000146 / myosin VII complex / phagolysosome assembly / inner ear receptor cell differentiation / protein localization => GO:0008104 / regulation of clathrin-dependent endocytosis / equilibrioception / mechanoreceptor differentiation / sensory perception of light stimulus / photoreceptor connecting cilium / actin filament-based movement / inner ear receptor cell stereocilium organization / sensory organ development / : / inner ear auditory receptor cell differentiation / sensory perception / stereocilium / cell projection organization / vesicle transport along actin filament / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / myosin complex / microfilament motor activity / ciliary base / inner ear morphogenesis / spectrin binding / lysosome organization / cochlea development / inner ear development / microvillus / cytoskeletal motor activity / photoreceptor outer segment / Cajal body / phagocytosis / photoreceptor inner segment / visual perception / ciliary basal body / actin filament organization / ADP binding / sensory perception of sound / intracellular protein transport / protein localization / actin filament binding / melanosome / actin cytoskeleton / actin binding / cell cortex / vesicle / calmodulin binding / nuclear speck / apical plasma membrane / lysosomal membrane / protein domain specific binding / centrosome / synapse / protein-containing complex binding / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
USH1G, SAM domain / MyTH4 domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails ...USH1G, SAM domain / MyTH4 domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / SAM domain (Sterile alpha motif) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / SH3 Domains / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / SH3 type barrels. / Src homology 3 domains / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Unconventional myosin-VIIa / pre-mRNA splicing regulator USH1G / Unconventional myosin-VIIa
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWu, L. / Pan, L.F. / Wei, Z.Y. / Zhang, M.J.
CitationJournal: Science / Year: 2011
Title: Structure of MyTH4-FERM domains in myosin VIIa tail bound to cargo.
Authors: Wu, L. / Pan, L. / Wei, Z. / Zhang, M.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin VIIa isoform 1
B: Usher syndrome type-1G protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,58813
Polymers84,5692
Non-polymers1,01911
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.864, 98.864, 242.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Myosin VIIa isoform 1


Mass: 74353.219 Da / Num. of mol.: 1 / Fragment: MyTH4-FERM-SH3 region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5MJ57, UniProt: P97479*PLUS
#2: Protein Usher syndrome type-1G protein / Scaffold protein containing ankyrin repeats and SAM domain


Mass: 10215.873 Da / Num. of mol.: 1 / Fragment: Central region of Sans, the CEN1 motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1G, SANS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q495M9
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02M MgCl2, 0.1M HEPES, pH 7.5, 22% (w/v) polyacrylic acid sodium salt 5100, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 34633 / Num. obs: 32761 / % possible obs: 99.57 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31
Reflection shellResolution: 2.801→2.874 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 31 / Num. unique all: 34633 / % possible all: 99.69

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.315 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 3.7 / σ(I): 3.7 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25903 1740 5 %RANDOM
Rwork0.22764 ---
all0.22922 34633 --
obs0.22922 32761 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.928 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 64 38 4990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225066
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9726852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.925610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23923.465228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83615855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9261535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213799
X-RAY DIFFRACTIONr_mcbond_it1.40223062
X-RAY DIFFRACTIONr_mcangle_it2.64534950
X-RAY DIFFRACTIONr_scbond_it3.3842004
X-RAY DIFFRACTIONr_scangle_it5.58561901
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 134 -
Rwork0.352 2418 -
obs--99.69 %

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