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- PDB-4p9t: Structure of the free form of the N-terminal VH1 domain of monome... -

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Basic information

Entry
Database: PDB / ID: 4p9t
TitleStructure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin
ComponentsCatenin alpha-2
KeywordsCELL ADHESION / Cytoskeletal protein / adherens junction / helix bundle
Function / homology
Function and homology information


radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / extrinsic component of postsynaptic membrane / modification of postsynaptic actin cytoskeleton / extrinsic component of presynaptic membrane / negative regulation of Arp2/3 complex-mediated actin nucleation / presynaptic active zone cytoplasmic component / Myogenesis / regulation of neuron migration / brain morphogenesis ...radial glia guided migration of Purkinje cell / regulation of synapse structural plasticity / extrinsic component of postsynaptic membrane / modification of postsynaptic actin cytoskeleton / extrinsic component of presynaptic membrane / negative regulation of Arp2/3 complex-mediated actin nucleation / presynaptic active zone cytoplasmic component / Myogenesis / regulation of neuron migration / brain morphogenesis / dendrite morphogenesis / parallel fiber to Purkinje cell synapse / regulation of neuron projection development / prepulse inhibition / postsynaptic density, intracellular component / axonogenesis / hippocampal mossy fiber to CA3 synapse / adherens junction / cell-cell adhesion / 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
IODIDE ION / DI(HYDROXYETHYL)ETHER / Catenin alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShibahara, T. / Hirano, Y. / Hakoshima, T.
CitationJournal: Febs Lett. / Year: 2015
Title: Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin.
Authors: Shibahara, T. / Hirano, Y. / Hakoshima, T.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,34038
Polymers115,8454
Non-polymers3,49534
Water68538
1
C: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,88810
Polymers28,9611
Non-polymers9279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,88810
Polymers28,9611
Non-polymers9279
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7829
Polymers28,9611
Non-polymers8218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catenin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7829
Polymers28,9611
Non-polymers8218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.777, 68.777, 207.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRchain A and (resseq 20:41 or resseq 56:260 )AA20 - 4122 - 43
12LYSLYSALAALAchain A and (resseq 20:41 or resseq 56:260 )AA56 - 26058 - 262
21ARGARGTHRTHRchain B and (resseq 20:41 or resseq 56:260 )BB20 - 4122 - 43
22LYSLYSALAALAchain B and (resseq 20:41 or resseq 56:260 )BB56 - 26058 - 262
31ARGARGTHRTHRchain C and (resseq 20:41 or resseq 56:260 )CC20 - 4122 - 43
32LYSLYSALAALAchain C and (resseq 20:41 or resseq 56:260 )CC56 - 26058 - 262
41ARGARGTHRTHRchain D and (resseq 20:41 or resseq 56:260 )DD20 - 4122 - 43
42LYSLYSALAALAchain D and (resseq 20:41 or resseq 56:260 )DD56 - 26058 - 262

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Components

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


Mass: 28961.299 Da / Num. of mol.: 4 / Fragment: UNP residues 13-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna2, Catna2 / Plasmid: pET-47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q61301
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 14, 2013
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38552 / % possible obs: 99.5 % / Redundancy: 5.7 % / Net I/σ(I): 46.2
Reflection shellHighest resolution: 2.5 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data scaling
MrBUMPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOV

1dov


Resolution: 2.5→45.177 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1891 5 %Random selection
Rwork0.2147 ---
obs0.2157 37854 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 82 38 6731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086715
X-RAY DIFFRACTIONf_angle_d0.929106
X-RAY DIFFRACTIONf_dihedral_angle_d14.8662330
X-RAY DIFFRACTIONf_chiral_restr0.031156
X-RAY DIFFRACTIONf_plane_restr0.0041181
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1626X-RAY DIFFRACTIONPOSITIONAL
12B1626X-RAY DIFFRACTIONPOSITIONAL0.01
13C1620X-RAY DIFFRACTIONPOSITIONAL0.009
14D1626X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56260.35141330.30872599X-RAY DIFFRACTION100
2.5626-2.63190.35451290.33932643X-RAY DIFFRACTION100
2.6319-2.70940.32091330.30982508X-RAY DIFFRACTION100
2.7094-2.79680.30611330.27032596X-RAY DIFFRACTION100
2.7968-2.89670.27831470.28512578X-RAY DIFFRACTION100
2.8967-3.01270.25931360.27562569X-RAY DIFFRACTION100
3.0127-3.14980.29821630.26462576X-RAY DIFFRACTION100
3.1498-3.31580.27661410.24042592X-RAY DIFFRACTION100
3.3158-3.52350.23371330.21922558X-RAY DIFFRACTION100
3.5235-3.79540.20131340.19532614X-RAY DIFFRACTION100
3.7954-4.17710.20041460.18412524X-RAY DIFFRACTION100
4.1771-4.78090.19131350.17492625X-RAY DIFFRACTION100
4.7809-6.02120.21511100.20042580X-RAY DIFFRACTION100
6.0212-45.18430.2251180.18292401X-RAY DIFFRACTION92

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