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- PDB-5xfl: Crystal structure of the force-sensing device region of alpha N-c... -

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Basic information

Entry
Database: PDB / ID: 5xfl
TitleCrystal structure of the force-sensing device region of alpha N-catenin
ComponentsCatenin alpha-2CTNNA2
KeywordsCELL ADHESION / MECHANOTRANSDUCTION / CYTOSKELETON
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / presynaptic active zone cytoplasmic component / Myogenesis / brain morphogenesis ...radial glia guided migration of Purkinje cell / extrinsic component of postsynaptic membrane / regulation of synapse structural plasticity / extrinsic component of presynaptic membrane / modification of postsynaptic actin cytoskeleton / negative regulation of Arp2/3 complex-mediated actin nucleation / regulation of neuron migration / presynaptic active zone cytoplasmic component / Myogenesis / brain morphogenesis / catenin complex / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / regulation of neuron projection development / postsynaptic density, intracellular component / prepulse inhibition / hippocampal mossy fiber to CA3 synapse / axonogenesis / adherens junction / cell-cell adhesion / beta-catenin binding / cell migration / actin filament binding / actin cytoskeleton / lamellipodium / basolateral plasma membrane / postsynaptic density / cadherin binding / axon / structural molecule activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Alpha-catenin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsHirano, Y. / Hakoshima, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Scientific Research on Innovative Area Structural Cell Biology, the Ministry of Education, Culture, Sports, Science and Technology Japan
Scientific Research for Young Scientists, the Ministry of Education, Culture, Sports, Science and Technology21770114 Japan
a research grant in the natural sciences from the Mitsubishi Foundation Japan
CitationJournal: Genes Cells / Year: 2018
Title: The force-sensing device region of alpha-catenin is an intrinsically disordered segment in the absence of intramolecular stabilization of the autoinhibitory form
Authors: Hirano, Y. / Amano, Y. / Yonemura, S. / Hakoshima, T.
History
DepositionApr 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Catenin alpha-2
B: Catenin alpha-2
C: Catenin alpha-2
D: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)166,9494
Polymers166,9494
Non-polymers00
Water5,675315
1
A: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)41,7371
Polymers41,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)41,7371
Polymers41,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)41,7371
Polymers41,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catenin alpha-2


Theoretical massNumber of molelcules
Total (without water)41,7371
Polymers41,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.728, 52.206, 154.310
Angle α, β, γ (deg.)90.00, 95.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Catenin alpha-2 / CTNNA2 / Alpha N-catenin


Mass: 41737.211 Da / Num. of mol.: 4 / Fragment: UNP residues 260-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna2, Catna2 / Plasmid: PET47B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61301
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 23, 2010 / Details: MIRRORS
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR , SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 76514 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.071 / Net I/σ(I): 21.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.487 / % possible all: 93.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: SAD / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.769 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3835 5 %RANDOM
Rwork0.224 ---
obs0.226 72343 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 46.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---0.33 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11031 0 0 315 11346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.96815051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5651418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94524.945542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.185152048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0741598
X-RAY DIFFRACTIONr_chiral_restr0.0980.21789
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1971.57101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19211422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.07234036
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3364.53629
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 258 -
Rwork0.293 4940 -
obs--91.58 %
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)
11.4598-0.6268-0.374.53513.21294.15160.0411-0.17230.14840.3306-0.2130.1580.0268-0.30070.17190.10280.0078-0.04910.2094-0.00210.195120.713.07860.368
25.2088-0.8442-4.04011.5210.40964.73430.20670.42170.392-0.2559-0.1568-0.4175-0.22170.2604-0.04990.16050.0757-0.0650.34230.08440.372146.358-1.33339.838
31.5223-0.26360.83312.7651-2.11275.60460.15130.299-0.1751-0.1759-0.1109-0.08150.3517-0.0539-0.04040.05330.0717-0.03270.1867-0.06540.142621.637-12.96637.622
41.8744-1.0832.37281.9191-2.24685.88250.1235-0.0255-0.0610.0073-0.0605-0.10730.2963-0.0607-0.0630.120.0054-0.03080.15670.01470.160378.569-37.41466.379
58.3375-1.98966.62231.4956-2.02525.93220.23220.3205-0.2274-0.1698-0.13190.13950.20730.0924-0.10030.12560.09310.00940.2645-0.0260.196149.546-25.4746.847
62.7829-0.229-1.03782.54510.57055.19370.11320.17070.24210.0845-0.14460.1072-0.4107-0.1690.03140.0840.0471-0.00310.19840.02710.174173.328-12.5343.452
72.7910.2909-3.09291.5827-0.8596.5690.09360.19160.0898-0.09210.0646-0.1425-0.32070.0944-0.15820.09150.0453-0.0110.3567-0.02670.188921.84512.3639.101
88.7201-3.5995-7.41932.49793.55727.41720.1048-0.58090.50090.07350.1257-0.0961-0.26150.1374-0.23050.14370.1506-0.0130.57450.07070.3112-7.6422.06128.807
93.6002-0.0160.31722.81340.43944.4930.06410.0651-0.1091-0.03570.06430.33220.2394-0.5756-0.12840.06010.0666-0.04720.3190.02090.22820.568-3.80132.616
104.97070.61672.25593.12420.9445.8864-0.08141.0436-0.4875-0.7612-0.02270.65940.6167-0.58890.10410.5301-0.0468-0.05660.8245-0.15360.484276.17-39.1615.558
115.549-1.63494.00292.5153-3.85298.26950.1836-0.3872-0.721-0.1286-0.1737-0.08590.8310.5561-0.00990.40910.24730.18930.66650.06620.5509104.92-45.91636.223
122.35470.2168-2.05711.8419-0.48375.09850.0941-0.05580.03960.0335-0.0692-0.2139-0.23730.6254-0.02480.05390.0389-0.01660.43830.0520.212695.308-20.08536.879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A271 - 394
2X-RAY DIFFRACTION2A395 - 504
3X-RAY DIFFRACTION3A505 - 629
4X-RAY DIFFRACTION4B271 - 394
5X-RAY DIFFRACTION5B395 - 504
6X-RAY DIFFRACTION6B505 - 630
7X-RAY DIFFRACTION7C271 - 394
8X-RAY DIFFRACTION8C395 - 504
9X-RAY DIFFRACTION9C505 - 629
10X-RAY DIFFRACTION10D271 - 394
11X-RAY DIFFRACTION11D395 - 504
12X-RAY DIFFRACTION12D505 - 631

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