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- PDB-4x25: Structural basis for mutation-induced destabilization of Profilin... -

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Basic information

Entry
Database: PDB / ID: 4x25
TitleStructural basis for mutation-induced destabilization of Profilin 1 in ALS
ComponentsProfilin-1
KeywordsPROTEIN BINDING / Human Profilin-1 M114T Mutant ALS
Function / homology
Function and homology information


synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway ...synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / neural tube closure / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Platelet degranulation / actin binding / cell cortex / actin cytoskeleton organization / blood microparticle / protein stabilization / cytoskeleton / cadherin binding / focal adhesion / glutamatergic synapse / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase ...Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsSilvas, T.V. / Shandilya, S.M.D. / Schiffer, C.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Structural basis for mutation-induced destabilization of profilin 1 in ALS.
Authors: Boopathy, S. / Silvas, T.V. / Tischbein, M. / Jansen, S. / Shandilya, S.M. / Zitzewitz, J.A. / Landers, J.E. / Goode, B.L. / Schiffer, C.A. / Bosco, D.A.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Profilin-1
B: Profilin-1


Theoretical massNumber of molelcules
Total (without water)30,0822
Polymers30,0822
Non-polymers00
Water2,846158
1
A: Profilin-1


Theoretical massNumber of molelcules
Total (without water)15,0411
Polymers15,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Profilin-1


Theoretical massNumber of molelcules
Total (without water)15,0411
Polymers15,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.690, 81.690, 65.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11B-228-

HOH

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Components

#1: Protein Profilin-1 / / Epididymis tissue protein Li 184a / Profilin I


Mass: 15041.128 Da / Num. of mol.: 2 / Mutation: M114T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: P07737
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.02 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 750 mM sodium citrate, 200 mM NaCl and 100 mM tris

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 16, 2013 / Details: Osmic Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→31.11 Å / Num. all: 12156 / Num. obs: 12156 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.4
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.49 / % possible all: 98.58

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Processing

Software
NameVersionClassification
HKL-3000data collection
xia2data scaling
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F1K

1f1k


Resolution: 2.23→31.108 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 581 4.78 %Random selection
Rwork0.1952 ---
obs0.1982 12156 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→31.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 158 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031945
X-RAY DIFFRACTIONf_angle_d0.6072650
X-RAY DIFFRACTIONf_dihedral_angle_d12.749646
X-RAY DIFFRACTIONf_chiral_restr0.022316
X-RAY DIFFRACTIONf_plane_restr0.003340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2303-2.45390.28711510.23752839X-RAY DIFFRACTION94
2.4539-2.80720.26091320.22352896X-RAY DIFFRACTION96
2.8072-3.530.251530.19662875X-RAY DIFFRACTION95
3.53-15.55440.19691450.16972931X-RAY DIFFRACTION95

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