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- PDB-4x1m: Structural basis for mutation-induced destabilization of Profilin... -

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Basic information

Entry
Database: PDB / ID: 4x1m
TitleStructural basis for mutation-induced destabilization of Profilin 1 in ALS
ComponentsProfilin-1
KeywordsPROTEIN BINDING / 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 / cytoskeleton / protein stabilization / 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: 2.17 Å
AuthorsSilvas, T.V. / Shandilya, S.M.D. / Schiffer, C.A.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS090352 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS078145 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS067206 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS073873 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM091743 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM091743-03S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM53846 United States
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 24, 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 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Apr 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 1.5Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Profilin-1


Theoretical massNumber of molelcules
Total (without water)14,9991
Polymers14,9991
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.650, 31.712, 60.539
Angle α, β, γ (deg.)90.00, 122.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14999.159 Da / Num. of mol.: 1 / Mutation: E117G
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.: 94 / 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: 39.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PFN1 crystals were grown by hanging drop vapor diffusion after mixing the PFN1 protein with a 1:1 ratio of reservoir solution at 298K for E117G. Reservoir solution for E117G contained 50 mM ...Details: PFN1 crystals were grown by hanging drop vapor diffusion after mixing the PFN1 protein with a 1:1 ratio of reservoir solution at 298K for E117G. Reservoir solution for E117G contained 50 mM KH2PO4, 41% (wt/vol) PEG 8,000 and 100 mM MES

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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: Mar 18, 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: 2.17→20 Å / Num. all: 6468 / Num. obs: 6468 / % possible obs: 99.5 % / Observed criterion σ(I): -2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.8
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 18.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIK

1fik


Resolution: 2.17→19.282 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 298 4.64 %Random selection
Rwork0.1965 ---
obs0.1973 6422 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→19.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 0 94 1009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003935
X-RAY DIFFRACTIONf_angle_d0.6681271
X-RAY DIFFRACTIONf_dihedral_angle_d12.151320
X-RAY DIFFRACTIONf_chiral_restr0.026154
X-RAY DIFFRACTIONf_plane_restr0.003161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1702-2.7330.25281630.19263024X-RAY DIFFRACTION100
2.733-19.28310.1931350.19833100X-RAY DIFFRACTION99

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