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- PDB-4x1l: Structural basis for mutation-induced destabilization of Profilin... -

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Basic information

Entry
Database: PDB / ID: 4x1l
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 / 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
PHOSPHATE ION / Profilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 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.USA / 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 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _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 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1662
Polymers15,0711
Non-polymers951
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.260, 31.840, 61.020
Angle α, β, γ (deg.)90.00, 122.66, 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: 15071.222 Da / Num. of mol.: 1
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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.03 Å3/Da / Density % sol: 39.32 %
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 WT. Reservoir solution for WT 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 WT. Reservoir solution for WT contained 50 mM KH2PO4, 36% (wt/vol) PEG 8,000 and 100 mM MES pH 6.0.

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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: Jun 5, 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: 2.16→27.9 Å / Num. all: 6584 / Num. obs: 6584 / % possible obs: 99.3 % / Observed criterion σ(I): -2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.3
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
xia2data scaling
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIK

1fik


Resolution: 2.16→27.895 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 308 4.68 %Random selection
Rwork0.2159 ---
obs0.2173 6579 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→27.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 5 64 975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002924
X-RAY DIFFRACTIONf_angle_d0.6161256
X-RAY DIFFRACTIONf_dihedral_angle_d10.829309
X-RAY DIFFRACTIONf_chiral_restr0.023150
X-RAY DIFFRACTIONf_plane_restr0.002158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1601-2.72110.28371460.25923104X-RAY DIFFRACTION99
2.7211-27.89750.23381620.20013167X-RAY DIFFRACTION99

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