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- PDB-5mv7: Structure of human Myosin 7b C-terminal MyTH4-FERM MF2 domain -

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Basic information

Entry
Database: PDB / ID: 5mv7
TitleStructure of human Myosin 7b C-terminal MyTH4-FERM MF2 domain
ComponentsUnconventional myosin-VIIb
KeywordsMOTOR PROTEIN / myosin / MyTh4-FERM / myosin tail
Function / homology
Function and homology information


apical cytoplasm / brush border assembly / sensory organ development / actin filament-based movement / myosin complex / microfilament motor activity / brush border / microvillus / actin filament organization / sensory perception of sound ...apical cytoplasm / brush border assembly / sensory organ development / actin filament-based movement / myosin complex / microfilament motor activity / brush border / microvillus / actin filament organization / sensory perception of sound / endocytosis / actin filament binding / actin cytoskeleton / cell differentiation / ATP binding / membrane / cytoplasm
Similarity search - Function
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 / IQ calmodulin-binding motif / Variant SH3 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 / 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. / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Unconventional myosin-VIIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsPlanelles-Herrero, V.J. / Sourigues, Y. / Titus, M.A. / Houdusse, A.
Funding support United States, France, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1244235 United States
French National Research AgencyANR-13-BSV8-0019-01 France
FRMING20140129255 France
Labex CelTisPhyBio11-LBX-0038 France
IDEX PSLANR-10-IDEX-0001-02-PSL France
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 15, 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 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin-VIIb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7456
Polymers60,1301
Non-polymers6155
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-35 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.670, 42.810, 118.370
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Unconventional myosin-VIIb


Mass: 60130.066 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: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 31-34% (v/v) PEG 400, 100 mM Tris-HCl pH 8.5 and 200 mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 22640 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 67.16 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.86
Reflection shellResolution: 2.44→2.53 Å / Mean I/σ(I) obs: 11.86 / CC1/2: 0.915 / % possible all: 93.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→35.17 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.885 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.439 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1132 5 %RANDOM
Rwork0.209 ---
obs0.211 22640 96.9 %-
Displacement parametersBiso mean: 66.66 Å2
Baniso -1Baniso -2Baniso -3
1--5.278 Å20 Å22.9525 Å2
2---18.2216 Å20 Å2
3---23.4997 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.44→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 37 139 4202
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15644HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes590HARMONIC5
X-RAY DIFFRACTIONt_it4167HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion524SEMIHARMONIC5
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_contact4664SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.333 137 5.01 %
Rwork0.272 2600 -
all0.275 2737 -
obs--88.95 %
Refinement TLS params.Method: refined / Origin x: 17.686 Å / Origin y: 0.834 Å / Origin z: 17.702 Å
111213212223313233
T0.1133 Å2-0.018 Å20.0986 Å2-0.2513 Å20.023 Å2--0.1819 Å2
L1.5951 °2-1.1822 °2-1.5055 °2-1.1403 °21.6953 °2--2.6678 °2
S0.0778 Å °-0.1482 Å °0.0646 Å °0.095 Å °-0.1427 Å °0.0112 Å °0.0797 Å °-0.5231 Å °0.0649 Å °
Refinement TLS groupSelection details: { A|1 - A|505 }

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