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- PDB-1v9d: Crystal structure of the core FH2 domain of mouse mDia1 -

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Basic information

Entry
Database: PDB / ID: 1v9d
TitleCrystal structure of the core FH2 domain of mouse mDia1
ComponentsDiaphanous protein homolog 1Transparency and translucency
KeywordsPROTEIN BINDING / helix bundle
Function / homology
Function and homology information


negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / actin nucleation / neuron projection retraction / RHO GTPases Activate Formins / protein localization to microtubule / profilin binding / cellular response to histamine / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / axon midline choice point recognition / regulation of cytoskeleton organization / brush border / synaptic vesicle endocytosis / ephrin receptor signaling pathway / cytoskeleton organization / actin filament polymerization / Neutrophil degranulation / actin filament / sensory perception of sound / brain development / protein localization / mitotic spindle / ruffle membrane / small GTPase binding / neuron projection development / presynapse / gene expression / actin binding / regulation of cell shape / actin cytoskeleton organization / transmembrane transporter binding / neuron projection / positive regulation of cell migration / centrosome / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #630 / Formin, FH2 domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #630 / Formin, FH2 domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein diaphanous homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsShimada, A. / Nyitrai, M. / Vetter, I.R. / Kuhlmann, D. / Bugyi, B. / Narumiya, S. / Geeves, M.A. / Wittinghofer, A.
CitationJournal: Mol.Cell / Year: 2004
Title: The core FH2 domain of diaphanous-related formins is an elongated actin binding protein that inhibits polymerization.
Authors: Shimada, A. / Nyitrai, M. / Vetter, I.R. / Kuhlmann, D. / Bugyi, B. / Narumiya, S. / Geeves, M.A. / Wittinghofer, A.
History
DepositionJan 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Diaphanous protein homolog 1
B: Diaphanous protein homolog 1
C: Diaphanous protein homolog 1
D: Diaphanous protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,3987
Polymers158,1104
Non-polymers2883
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.430, 124.521, 229.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Diaphanous protein homolog 1 / Transparency and translucency / Diaphanous-related formin 1 / DRF1 / mDIA1 / p140mDIA


Mass: 39527.453 Da / Num. of mol.: 4 / Fragment: core FH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: O08808
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG3350, sodium sulfate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 %(v/v)PEG33501reservoir
3200 mM1reservoirNa2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 73264 / Num. obs: 73264 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 406569 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 5.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.12 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 7136 RANDOM
Rwork0.236 --
all0.239 70566 -
obs0.239 70566 -
Refinement stepCycle: LAST / Resolution: 2.6→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9872 0 15 192 10079
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.2668 / Rfactor Rwork: 0.2299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0064
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.12
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.74

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