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- PDB-2bap: Crystal structure of the N-terminal mDia1 Armadillo Repeat Region... -

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Basic information

Entry
Database: PDB / ID: 2bap
TitleCrystal structure of the N-terminal mDia1 Armadillo Repeat Region and Dimerisation Domain in complex with the mDia1 autoregulatory domain (DAD)
Components(Diaphanous protein homolog 1Transparency and translucency) x 2
KeywordsSIGNALING PROTEIN / Armadillo Repeats / all helical
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
Formin, FH3 diaphanous 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 ...Formin, FH3 diaphanous 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Recoverin; domain 1 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein diaphanous homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLammers, M. / Rose, R. / Scrima, A. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2005
Title: The regulation of mDia1 by autoinhibition and its release by Rho*GTP.
Authors: Lammers, M. / Rose, R. / Scrima, A. / Wittinghofer, A.
History
DepositionOct 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Diaphanous protein homolog 1
A: Diaphanous protein homolog 1
D: Diaphanous protein homolog 1
C: Diaphanous protein homolog 1


Theoretical massNumber of molelcules
Total (without water)85,9894
Polymers85,9894
Non-polymers00
Water0
1
A: Diaphanous protein homolog 1
C: Diaphanous protein homolog 1

A: Diaphanous protein homolog 1
C: Diaphanous protein homolog 1


Theoretical massNumber of molelcules
Total (without water)85,9894
Polymers85,9894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
2
B: Diaphanous protein homolog 1
D: Diaphanous protein homolog 1

B: Diaphanous protein homolog 1
D: Diaphanous protein homolog 1


Theoretical massNumber of molelcules
Total (without water)85,9894
Polymers85,9894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Unit cell
Length a, b, c (Å)138.450, 138.450, 210.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12D
22C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHISBA135 - 4351 - 301
21SERSERHISHISAB135 - 4351 - 301
12GLYGLYPHEPHEDC1180 - 119536 - 51
22GLYGLYPHEPHECD1180 - 119536 - 51

NCS ensembles :
ID
1
2

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Components

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


Mass: 36534.020 Da / Num. of mol.: 2 / Fragment: mDia1 N-terminal regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Diaph1, Diap1 / Plasmid: pGEX4-T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#2: Protein Diaphanous protein homolog 1 / Transparency and translucency / Diaphanous-related formin 1 / DRF1 / mDIA1 / p140mDIA


Mass: 6460.428 Da / Num. of mol.: 2 / Fragment: mDia1 autoregulatory domain, DAD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Diaph1, Diap1 / Plasmid: pGEX4-T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08808

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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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 3.7 M NaFormiate pH 7.1, 100 mM HEPES pH 7.1, 4% (w/v) PEG5000-MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 28, 2005
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 18490 / % possible obs: 81.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 16.79
Reflection shellResolution: 3.3→3.4 Å / % possible obs: 0 % / Num. measured obs: 0 / Num. unique obs: 0 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Z2C

1z2c


Resolution: 3.3→19.98 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.839 / SU B: 38.004 / SU ML: 0.621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.364 925 5 %RANDOM
Rwork0.288 ---
all0.292 18490 --
obs0.292 18490 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.189 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 0 0 4960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225031
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.996770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.41325.02247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36415983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4591536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023708
X-RAY DIFFRACTIONr_nbd_refined0.2410.22619
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2156
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.27
X-RAY DIFFRACTIONr_mcbond_it0.4111.53192
X-RAY DIFFRACTIONr_mcangle_it0.71824974
X-RAY DIFFRACTIONr_scbond_it0.69432018
X-RAY DIFFRACTIONr_scangle_it1.1324.51796
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberRmsTypeWeight
1B23660.61MEDIUM POSITIONAL0.5
1B23661.52MEDIUM THERMAL2
2D1110.48MEDIUM POSITIONAL0.5
2D1110.71MEDIUM THERMAL2
LS refinement shellResolution: 3.3→3.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 65 -
Rwork0.373 1231 -
all-1296 -
obs--100 %

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