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- PDB-6jle: Crystal structure of MORN4/Myo3a complex -

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Basic information

Entry
Database: PDB / ID: 6jle
TitleCrystal structure of MORN4/Myo3a complex
Components
  • MORN repeat-containing protein 4
  • Myosin-IIIa
KeywordsMOTOR PROTEIN / PROTEIN BINDING / PROTEIN TRANSPORT
Function / homology
Function and homology information


plus-end directed microfilament motor activity / protein serine/threonine kinase activity => GO:0004674 / cochlea morphogenesis / stereocilium tip / filopodium tip / response to stimulus / myosin complex / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / microfilament motor activity ...plus-end directed microfilament motor activity / protein serine/threonine kinase activity => GO:0004674 / cochlea morphogenesis / stereocilium tip / filopodium tip / response to stimulus / myosin complex / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / microfilament motor activity / filamentous actin / response to axon injury / visual perception / filopodium / sensory perception of sound / ADP binding / actin binding / protein autophosphorylation / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / protein serine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Class III myosin, motor domain / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / IQ calmodulin-binding motif / 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. ...Class III myosin, motor domain / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat / IQ calmodulin-binding motif / 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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / MORN repeat-containing protein 4 / Myosin-IIIa
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsLi, J. / Liu, H. / Raval, M.H. / Wan, J. / Yengo, C.M. / Liu, W. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700673 China
CitationJournal: Structure / Year: 2019
Title: Structure of the MORN4/Myo3a Tail Complex Reveals MORN Repeats as Protein Binding Modules.
Authors: Li, J. / Liu, H. / Raval, M.H. / Wan, J. / Yengo, C.M. / Liu, W. / Zhang, M.
History
DepositionMar 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 27, 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

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Assembly

Deposited unit
A: MORN repeat-containing protein 4
E: Myosin-IIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5327
Polymers21,8712
Non-polymers6615
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-15 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.735, 73.735, 48.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein MORN repeat-containing protein 4


Mass: 16226.919 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Morn4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PGF2
#2: Protein/peptide Myosin-IIIa


Mass: 5644.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NEV4, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.5 M ammonium sulfate, 1.0 M lithium sulfate, 0.1 M sodium citrate tribasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 37810 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Χ2: 1.616 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.587.21.13819140.6580.4551.2261.268100
1.58-1.617.21.11418670.6630.4451.2011.301100
1.61-1.647.20.9418630.7250.3741.0121.334100
1.64-1.677.30.82118720.8120.3270.8841.296100
1.67-1.717.30.65218700.8540.2580.7011.322100
1.71-1.757.30.5718520.8920.2250.6141.344100
1.75-1.797.30.50119380.910.1980.541.332100
1.79-1.847.30.37418520.950.1480.4021.362100
1.84-1.897.40.30718880.9650.1210.331.378100
1.89-1.957.40.2318990.9810.0910.2471.496100
1.95-2.027.40.18718660.9870.0740.2011.705100
2.02-2.17.40.15218940.9870.060.1631.905100
2.1-2.27.30.12918970.9910.0510.1382.03100
2.2-2.327.20.1118810.9930.0440.1192.283100
2.32-2.467.20.10119020.9940.040.1092.483100
2.46-2.657.30.07918920.9960.0310.0852.121100
2.65-2.9270.05318710.9980.0220.0571.62999.9
2.92-3.347.50.04119070.9990.0160.0441.558100
3.34-4.217.60.03519350.9990.0140.0371.627100
4.21-507.30.03419500.9990.0140.0361.52598.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→32.975 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.42
RfactorNum. reflection% reflection
Rfree0.186 1961 5.19 %
Rwork0.1608 --
obs0.1621 37784 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.26 Å2 / Biso mean: 25.6637 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 1.55→32.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 44 133 1683
Biso mean--34.83 32.95 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071629
X-RAY DIFFRACTIONf_angle_d0.9312189
X-RAY DIFFRACTIONf_chiral_restr0.058216
X-RAY DIFFRACTIONf_plane_restr0.005294
X-RAY DIFFRACTIONf_dihedral_angle_d18.398972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5499-1.58860.2391410.209625572698100
1.5886-1.63160.25371440.193825402684100
1.6316-1.67960.21611420.175925162658100
1.6796-1.73380.23081660.164225292695100
1.7338-1.79580.17641450.161925492694100
1.7958-1.86770.23171010.14925812682100
1.8677-1.95270.17211580.142725472705100
1.9527-2.05560.18261410.134925232664100
2.0556-2.18430.17891500.14625232673100
2.1843-2.3530.17641570.146825642721100
2.353-2.58970.18041070.159325982705100
2.5897-2.96420.19011350.171325832718100
2.9642-3.73370.17561460.169725772723100
3.7337-32.98270.18091280.16022636276499

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