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- PDB-2v8f: Mouse Profilin IIa in complex with a double repeat from the FH1 d... -

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Basic information

Entry
Database: PDB / ID: 2v8f
TitleMouse Profilin IIa in complex with a double repeat from the FH1 domain of mDia1
Components
  • PROFILIN-2
  • PROTEIN DIAPHANOUS HOMOLOG 1
KeywordsPROTEIN BINDING / ALTERNATIVE SPLICING / PROTEIN-BINDING / CYTOPLASM / ACETYLATION / CYTOSKELETON / ACTIN-BINDING
Function / homology
Function and homology information


Signaling by ROBO receptors / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / negative regulation of ruffle assembly / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle ...Signaling by ROBO receptors / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / negative regulation of ruffle assembly / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction / modification of postsynaptic actin cytoskeleton / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / protein localization to microtubule / profilin binding / cellular response to histamine / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / axon midline choice point recognition / regulation of synaptic vesicle exocytosis / positive regulation of actin filament polymerization / regulation of cytoskeleton organization / brush border / synaptic vesicle endocytosis / actin monomer binding / ephrin receptor signaling pathway / positive regulation of stress fiber assembly / cytoskeleton organization / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / presynaptic modulation of chemical synaptic transmission / Neutrophil degranulation / actin filament / sensory perception of sound / brain development / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / protein localization / mitotic spindle / ruffle membrane / small GTPase binding / neuron projection development / presynapse / positive regulation of peptidyl-serine phosphorylation / gene expression / actin binding / regulation of cell shape / actin cytoskeleton organization / postsynapse / transmembrane transporter binding / protein stabilization / cytoskeleton / positive regulation of cell migration / neuron projection / centrosome / glutamatergic synapse / ATP hydrolysis activity / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Profilin1/2/3, vertebrate / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain ...Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Profilin1/2/3, vertebrate / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / : / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / Armadillo-like helical / Armadillo-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Protein diaphanous homolog 1 / Profilin-2 / Profilin-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKursula, P. / Kursula, I. / Downer, J. / Witke, W. / Wilmanns, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: High-Resolution Structural Analysis of Mammalian Profilin 2A Complex Formation with Two Physiological Ligands: The Formin Homology 1 Domain of Mdia1 and the Proline-Rich Domain of Vasp.
Authors: Kursula, P. / Kursula, I. / Massimi, M. / Song, Y.H. / Downer, J. / Stanley, W.A. / Witke, W. / Wilmanns, M.
History
DepositionAug 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROFILIN-2
B: PROFILIN-2
C: PROTEIN DIAPHANOUS HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,79111
Polymers32,1363
Non-polymers6558
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-91.3 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.380, 37.270, 88.750
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein PROFILIN-2 / / PROFILIN IIA


Mass: 15064.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3V171, UniProt: Q9JJV2*PLUS
#2: Protein/peptide PROTEIN DIAPHANOUS HOMOLOG 1 / DIAPHANOUS-RELATED FORMIN-1 / DRF1 / P140MDIA / MDIA1


Mass: 2007.414 Da / Num. of mol.: 1 / Fragment: FH1 DOMAIN, RESIDUES 635-655 / Source method: obtained synthetically
Details: TWO PROLINE-RICH REPEATS DERIVED FROM THE MOUSE HOMOLOGUE OF DIAPHANOUS 1 (MDIA1).
Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: O08808

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Non-polymers , 5 types, 365 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 1.65 Å3/Da / Density % sol: 25.01 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0408
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 93713 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 75.4

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Processing

Software
NameClassification
SHELXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D1J

1d1j


Resolution: 1.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: FINAL ROUND OF B FACTOR REFINEMENT DONE IN PHENIX.REFINE
RfactorNum. reflection% reflectionSelection details
Rfree0.173 -2 %RANDOM
obs0.146 -92.8 %-
all-93713 --
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 36 357 2591

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