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- PDB-1awi: HUMAN PLATELET PROFILIN COMPLEXED WITH THE L-PRO10 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1awi
TitleHUMAN PLATELET PROFILIN COMPLEXED WITH THE L-PRO10 PEPTIDE
Components
  • L-PRO10
  • PROFILIN
KeywordsCOMPLEX (ACTIN-BINDING PROTEIN/PEPTIDE) / PROFILIN / POLY-L-PROLINE / ACTIN CYTOSKELETON / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) complex
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 / MIR / Resolution: 2.2 Å
AuthorsMahoney, N.M. / Almo, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of the profilin-poly-L-proline complex involved in morphogenesis and cytoskeletal regulation.
Authors: Mahoney, N.M. / Janmey, P.A. / Almo, S.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Human Platelet Profilin Complexed with an Oligo Proline Peptide
Authors: Mahoney, N.M. / Almo, S.C.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Erratum. Structure of the Profilin-Poly-L-Proline Complex Involved in Morphogenesis and Cytoskeletal Regulation
Authors: Mahoney, N.M. / Janmey, P.A. / Almo, S.C.
History
DepositionOct 2, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
B: PROFILIN
P: L-PRO10


Theoretical massNumber of molelcules
Total (without water)30,7273
Polymers30,7273
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.250, 97.640, 39.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROFILIN /


Mass: 14868.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PLATELET / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: PMW172 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Tissue (production host): PLATELET / References: UniProt: P07737
#2: Protein/peptide L-PRO10


Mass: 989.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42 %
Crystal growpH: 8
Details: PROTEIN CRYSTALLIZED IN 2.0 MOLAR AMMONIUM SULFATE 0.1 MOLAR TRIS PH 8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 13062 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 4.46 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.053 / % possible all: 54.2

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Processing

Software
NameVersionClassification
PHASESX-PLORphasing
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / σ(F): 2
Details: PEPTIDE ORIENTATION WAS DETERMINED BY AN IODOTYROSINE LABELLED PEPTIDE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.305 -10 %RANDOM
Rwork0.204 ---
obs0.204 11577 94.3 %-
Displacement parametersBiso mean: 23.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12217 0 0 22 12239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.497
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→8 Å /
Num. reflection% reflection
Rwork1255 -
obs-94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO

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