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- PDB-5mv8: Structure of human Myosin 7b C-terminal MyTH4-FERM domain in comp... -

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Basic information

Entry
Database: PDB / ID: 5mv8
TitleStructure of human Myosin 7b C-terminal MyTH4-FERM domain in complex with harmonin-a PDZ3 domain
Components
  • Unconventional myosin-VIIb
  • cDNA FLJ51329, highly similar to Harmonin
KeywordsMOTOR PROTEIN / myosin / harmonin / myosin tail / PDZ
Function / homology
Function and homology information


apical cytoplasm / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip ...apical cytoplasm / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization / sensory organ development / actin filament-based movement / inner ear auditory receptor cell differentiation / stereocilium / photoreceptor cell maintenance / myosin complex / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / spectrin binding / microfilament motor activity / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / photoreceptor inner segment / actin filament organization / sensory perception of sound / cilium / endocytosis / G2/M transition of mitotic cell cycle / actin filament binding / actin cytoskeleton / apical part of cell / protein-containing complex assembly / cell differentiation / cytoskeleton / synapse / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Harmonin, N-terminal domain / Harmonin / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails ...Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Harmonin, N-terminal domain / Harmonin / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / Variant SH3 domain / 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. / PDZ domain / Pdz3 Domain / IQ motif, EF-hand binding site / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
cDNA FLJ51329, highly similar to Harmonin / Unconventional myosin-VIIb / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYu, I. / Sourigues, Y. / Titus, M.A. / Houdusse, A.
CitationJournal: Nat Commun / Year: 2017
Title: Myosin 7 and its adaptors link cadherins to actin.
Authors: Yu, I.M. / Planelles-Herrero, V.J. / Sourigues, Y. / Moussaoui, D. / Sirkia, H. / Kikuti, C. / Stroebel, D. / Titus, M.A. / Houdusse, A.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Unconventional myosin-VIIb
B: cDNA FLJ51329, highly similar to Harmonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5989
Polymers75,0212
Non-polymers5777
Water6,846380
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-17 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 42.560, 118.170
Angle α, β, γ (deg.)90.00, 98.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Unconventional myosin-VIIb


Mass: 60773.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO7B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIF6
#2: Protein cDNA FLJ51329, highly similar to Harmonin


Mass: 14247.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DV53, UniProt: Q9Y6N9*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 7% (w/v) PEG 4000, 0.1 M HEPES pH 7.5, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.906032 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906032 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 53567 / % possible obs: 95 % / Redundancy: 6.4 % / Biso Wilson estimate: 36.56 Å2 / CC1/2: 0.998 / Rsym value: 0.097 / Net I/σ(I): 12.77
Reflection shellMean I/σ(I) obs: 1 / CC1/2: 0.543 / Rsym value: 1.243 / % possible all: 61

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→35.33 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2676 5 %RANDOM
Rwork0.19 ---
obs0.191 53567 94.9 %-
Displacement parametersBiso mean: 44.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.419 Å20 Å2-2.7026 Å2
2---7.2416 Å20 Å2
3---10.6606 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.88→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 37 380 5137
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014958HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996755HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1697SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes734HARMONIC5
X-RAY DIFFRACTIONt_it4958HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion15.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion647SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6098SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 -4.89 %
Rwork0.411 1419 -
all0.411 1492 -
obs--36.17 %
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)
10.1533-0.06530.01140.359-0.18951.94770.0490.03460.0029-0.15510.0084-0.0382-0.02290.3167-0.0574-0.086-0.03310.0037-0.1433-0.0158-0.09126.9957-0.171422.3494
24.3641-1.79070.31861.7399-0.36450.72190.00790.4857-0.3233-0.125-0.04950.00260.09650.16130.0416-0.1461-0.05230.00110.0037-0.0715-0.099332.7583-15.402638.6025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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