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- PDB-5et0: Crystal structure of Myo3b-ARB2 in complex with Espin1-AR -

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Basic information

Entry
Database: PDB / ID: 5et0
TitleCrystal structure of Myo3b-ARB2 in complex with Espin1-AR
Components
  • Espin
  • Myosin-IIIb
KeywordsPROTEIN BINDING/MOTOR PROTEIN / Unconventional myosin / protein binding / signaling / PROTEIN BINDING-MOTOR PROTEIN complex
Function / homology
Function and homology information


microvillar actin bundle assembly / negative regulation of cytoskeleton organization / regulation of actin filament length / parallel actin filament bundle assembly / actin filament network formation / cochlea morphogenesis / stereocilium tip / stereocilium bundle / filopodium tip / stereocilium ...microvillar actin bundle assembly / negative regulation of cytoskeleton organization / regulation of actin filament length / parallel actin filament bundle assembly / actin filament network formation / cochlea morphogenesis / stereocilium tip / stereocilium bundle / filopodium tip / stereocilium / auditory receptor cell stereocilium organization / anchoring junction / myosin complex / response to stimulus / positive regulation of filopodium assembly / microfilament motor activity / filamentous actin / microvillus / actin filament bundle assembly / brush border / photoreceptor outer segment / photoreceptor inner segment / visual perception / locomotory behavior / sensory perception of sound / peptidyl-threonine phosphorylation / SH3 domain binding / actin filament binding / actin cytoskeleton / actin binding / peptidyl-serine phosphorylation / dendritic spine / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Class III myosin, motor domain / Ankyrin repeats (many copies) / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / IQ calmodulin-binding motif / Ankyrin repeats (many copies) / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain ...Class III myosin, motor domain / Ankyrin repeats (many copies) / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / IQ calmodulin-binding motif / Ankyrin repeats (many copies) / 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 / Kinesin motor domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLiu, H. / Li, J. / Liu, W. / Zhang, M.
CitationJournal: Elife / Year: 2016
Title: Myosin III-mediated cross-linking and stimulation of actin bundling activity of Espin
Authors: Liu, H. / Li, J. / Raval, M.H. / Yao, N. / Deng, X. / Lu, Q. / Nie, S. / Feng, W. / Wan, J. / Yengo, C.M. / Liu, W. / Zhang, M.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Espin
B: Myosin-IIIb
C: Espin
D: Myosin-IIIb


Theoretical massNumber of molelcules
Total (without water)88,3054
Polymers88,3054
Non-polymers00
Water41423
1
A: Espin
B: Myosin-IIIb


Theoretical massNumber of molelcules
Total (without water)44,1522
Polymers44,1522
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-8 kcal/mol
Surface area15230 Å2
MethodPISA
2
C: Espin
D: Myosin-IIIb


Theoretical massNumber of molelcules
Total (without water)44,1522
Polymers44,1522
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-7 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.740, 68.780, 173.450
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Espin / / Ectoplasmic specialization protein


Mass: 37994.605 Da / Num. of mol.: 2 / Fragment: UNP residues 1-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Espn / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ET47
#2: Protein Myosin-IIIb


Mass: 6157.858 Da / Num. of mol.: 2 / Fragment: UNP residues 1252-1305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo3b / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EG27
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.6 M Ammonium Sulfate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→173.45 Å / Num. obs: 39636 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 38.59 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.12 / Rsym value: 0.103 / Χ2: 1.762 / Net I/av σ(I): 5.171 / Net I/σ(I): 7.7 / Num. measured all: 148562
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.423.80.7990.82226458660.4690.7991.996.6
2.42-2.573.80.4671.42089254970.2740.4672.995.9
2.57-2.753.70.3551.41915552170.2210.3553.996.4
2.75-2.973.80.1843.91798647390.1080.1845.694.8
2.97-3.253.70.1155.91649044180.0680.1157.994.9
3.25-3.643.70.0946.21396738260.0570.09411.290.5
3.64-4.23.70.0766.71209232630.0460.07614.588.9
4.2-5.143.80.05810.31197631160.0340.05815.999
5.14-7.273.80.05511.1929524390.0330.05515.299.2
7.27-34.693.50.04115444512550.0250.04116.690.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALAdata scaling
PHASERphasing
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ET1

5et1


Resolution: 2.3→34.69 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1925 4.86 %
Rwork0.2232 --
obs0.2247 39585 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.62 Å2 / Biso mean: 60.5109 Å2 / Biso min: 22.46 Å2
Refinement stepCycle: final / Resolution: 2.3→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 0 23 5008
Biso mean---38.38 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015096
X-RAY DIFFRACTIONf_angle_d1.1116971
X-RAY DIFFRACTIONf_chiral_restr0.061808
X-RAY DIFFRACTIONf_plane_restr0.009916
X-RAY DIFFRACTIONf_dihedral_angle_d11.6252939
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.31091420.26822757289996
2.3575-2.42130.32281360.26382678281496
2.4213-2.49250.28721560.25682720287696
2.4925-2.57290.32231620.25242635279795
2.5729-2.66480.23851250.27122783290896
2.6648-2.77150.27091080.26282662277095
2.7715-2.89760.281450.26332688283395
2.8976-3.05020.2721300.24822733286395
3.0502-3.24120.28681440.25032622276694
3.2412-3.49130.26711250.24242625275092
3.4913-3.84220.24121330.21952334246783
3.8422-4.39720.22221200.18992821294197
4.3972-5.53640.24391440.1872822296699
5.5364-34.69390.2151550.19652780293595
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)
10.28-0.3077-0.00310.62660.50890.8789-0.0320.1782-0.13010.03540.07770.0970.18480.04990.54411.1983-0.30920.70610.6099-0.30360.906255.0696-50.732374.1945
20.55490.8235-0.39192.1732-1.88882.1914-0.35510.4501-0.26710.2360.18230.47660.3695-1.0371-0.0440.542-0.11730.26530.7305-0.09950.48850.2569-21.120473.68
34.58531.6177-0.70534.913-0.19644.7748-0.2021-0.19290.00540.13930.0701-0.2453-0.21590.10070.11840.24070.0730.00050.25970.02550.189167.9319-1.408155.2358
42.9382-1.44170.23035.6645-1.11482.2801-0.75830.8354-0.9879-0.4571-0.0791-0.41830.943-0.03290.76680.8321-0.13220.37790.752-0.08520.675662.4241-29.269170.1494
55.68581.0321-0.7114.949-1.53496.5820.3024-0.86321.0786-0.2173-0.7427-0.3191-1.0807-0.01860.15250.70420.0397-0.19460.4791-0.09310.709242.311-39.270416.5382
61.5515-0.2105-0.24234.538-2.54392.8878-0.36260.139-0.0425-0.7814-0.02820.0082-0.3499-0.28370.36231.22250.2059-0.31520.6173-0.25190.693237.6477-10.466117.4206
72.21641.76791.98681.6271.18162.53010.1465-0.1351-0.0062-0.1327-0.0780.14680.1687-0.0706-0.01581.23240.2739-0.67780.591-0.25370.971636.8898-17.42712.2677
80.039-0.05910.11880.456-0.05620.3929-0.2811-0.1680.37610.10230.0850.0363-0.5621-0.30740.41061.03430.326-0.62250.5372-0.21380.740932.8908-28.43078.1484
91.2779-0.99510.51262.7073-2.38352.308-0.2469-0.34110.1055-0.3310.1850.5159-0.194-1.2009-0.07370.4450.088-0.18280.7204-0.06790.397229.8301-50.989914.3615
104.328-1.66241.09214.70270.18094.2117-0.14810.3025-0.2181-0.35790.07780.01450.3705-0.15540.05120.278-0.10290.01290.31460.00960.193345.0771-67.714129.0769
118.8891-2.26470.71969.4081-2.439.0326-0.1916-0.12670.29780.2192-0.1815-0.79490.00840.81220.34650.18390.0245-0.0620.44890.06170.306657.4147-67.172739.0804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 90 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 228 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 331 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1288 through 1307 )B0
5X-RAY DIFFRACTION5chain 'D' and (resid 1288 through 1307 )D0
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 23 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 24 through 57 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 58 through 116 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 117 through 228 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 229 through 307 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 308 through 331 )C0

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