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- PDB-5f3y: Crystal Structure of Myo7b N-MyTH4-FERM-SH3 in complex with Anks4b CEN -

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Basic information

Entry
Database: PDB / ID: 5f3y
TitleCrystal Structure of Myo7b N-MyTH4-FERM-SH3 in complex with Anks4b CEN
Components
  • Ankyrin repeat and SAM domain-containing protein 4B
  • Unconventional myosin-VIIb
KeywordsMOTOR PROTEIN/PROTEIN BINDING / MOTOR PROTEIN / PROTEIN BINDING / STRUCTURAL PROTEIN / PROTEIN TRANSPORT / MOTOR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


protein localization to microvillus / apical cytoplasm / brush border assembly / myosin complex / microvillus / brush border / cytoskeletal motor activity / response to endoplasmic reticulum stress / actin binding / protein-containing complex assembly ...protein localization to microvillus / apical cytoplasm / brush border assembly / myosin complex / microvillus / brush border / cytoskeletal motor activity / response to endoplasmic reticulum stress / actin binding / protein-containing complex assembly / cell differentiation / endoplasmic reticulum membrane / ATP binding / plasma membrane
Similarity search - Function
ANKS4B, SAM domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. ...ANKS4B, SAM domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / IRS-type PTB domain / PTB domain (IRS-1 type) / IQ calmodulin-binding motif / SAM domain (Sterile alpha motif) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Sterile alpha motif. / Sterile alpha motif domain / Kinesin motor domain superfamily / 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 / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ankyrin repeat and SAM domain-containing protein 4B / Unconventional myosin-VIIb
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.409 Å
AuthorsLi, J. / He, Y. / Lu, Q. / Zhang, M.
CitationJournal: Dev.Cell / Year: 2016
Title: Mechanistic Basis of Organization of the Harmonin/USH1C-Mediated Brush Border Microvilli Tip-Link Complex
Authors: Li, J. / He, Y. / Lu, Q. / Zhang, M.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 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: Unconventional myosin-VIIb
B: Ankyrin repeat and SAM domain-containing protein 4B


Theoretical massNumber of molelcules
Total (without water)81,5982
Polymers81,5982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-14 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.516, 197.516, 97.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Unconventional myosin-VIIb


Mass: 69985.125 Da / Num. of mol.: 1 / Fragment: N-MyTH4-FERM-SH3, UNP residues 962-1578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7b / Production host: Escherichia coli (E. coli) / References: UniProt: Q99MZ6
#2: Protein Ankyrin repeat and SAM domain-containing protein 4B / ANKS4B


Mass: 11613.118 Da / Num. of mol.: 1 / Fragment: CEN, UNP residues 252-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anks4b, Harp / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3X6

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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: 5.84 Å3/Da / Density % sol: 78.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%(w/v) Pentaerythritol ethoxylate (3/4 EO/OH), 0.1 M MES
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 24972 / % possible obs: 92.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 92.1 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.109 / Χ2: 1.651 / Net I/av σ(I): 19.612 / Net I/σ(I): 8.7 / Num. measured all: 169291
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.464.90.88812620.6570.4190.9871.46495.7
3.46-3.525.10.70112510.7240.3250.7781.60495.5
3.52-3.595.20.49412750.690.2290.5481.70495.4
3.59-3.665.30.35312280.7480.1690.3952.12694.5
3.66-3.745.30.3112490.8340.1480.3461.96993.9
3.74-3.835.30.3312270.8670.1540.3661.68694.2
3.83-3.925.90.43612470.8960.1880.4781.66693.9
3.92-4.036.30.32312500.9480.1340.3521.694.3
4.03-4.156.40.26812390.970.1090.2911.63193.7
4.15-4.286.70.22612110.9760.0910.2441.60491.3
4.28-4.446.80.16712320.9740.070.1822.01893
4.44-4.617.10.12512250.9860.050.1361.72791.3
4.61-4.827.30.12312290.9930.0470.1331.67292.5
4.82-5.087.60.11112760.9950.040.1191.53694
5.08-5.480.09912520.9960.0340.1051.51593.8
5.4-5.818.30.10112580.9960.0340.1071.62393.3
5.81-6.48.60.09912630.9970.0330.1051.77993
6.4-7.328.60.07512700.9970.0250.0791.64492
7.32-9.218.60.03912690.9990.0130.0421.34290.8
9.21-508.20.03112590.9990.0110.0331.44984.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(1.10_2142: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PVL

3pvl


Resolution: 3.409→30.718 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1288 5.2 %
Rwork0.2411 23493 -
obs0.2432 24781 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.33 Å2 / Biso mean: 93.211 Å2 / Biso min: 38.97 Å2
Refinement stepCycle: final / Resolution: 3.409→30.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 0 0 4041
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084143
X-RAY DIFFRACTIONf_angle_d1.1115700
X-RAY DIFFRACTIONf_chiral_restr0.062697
X-RAY DIFFRACTIONf_plane_restr0.008719
X-RAY DIFFRACTIONf_dihedral_angle_d13.9432401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4088-3.54510.38651320.36022515264791
3.5451-3.70620.34951390.29972664280395
3.7062-3.90120.34021410.29912611275294
3.9012-4.14510.36341340.3052571270592
4.1451-4.46430.27921490.25732554270391
4.4643-4.91190.23751500.19322584273492
4.9119-5.61890.27231480.2122650279894
5.6189-7.0650.29481480.24092673282193
7.065-30.71890.21951470.19352671281889
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)
12.76251.00251.20580.5460.16070.8920.10370.1651-0.6675-0.30460.1597-0.16860.36440.3477-0.40770.4570.0583-0.05231.0982-0.06381.06234.26151.2034-4.7002
22.1260.91991.30151.95581.09831.79830.0284-0.82120.02580.0764-0.1914-0.1055-0.3162-0.1583-0.06620.5054-0.1445-0.09110.6951-0.01360.5979-36.732152.1259-9.9929
32.1426-1.00811.07474.6048-2.82772.6009-1.7857-1.5105-0.39520.72210.39060.1832-0.2988-0.18760.58241.4607-0.2864-0.31141.91090.41351.8086-24.796558.29055.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 972 through 1251 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1252 through 1559 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 263 through 275 )B0

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