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- PDB-2bnx: Crystal structure of the dimeric regulatory domain of mouse diaph... -

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Basic information

Entry
Database: PDB / ID: 2bnx
TitleCrystal structure of the dimeric regulatory domain of mouse diaphaneous-related formin (DRF), mDia1
ComponentsDIAPHANOUS PROTEIN HOMOLOG 1Transparency and translucency
KeywordsSTRUCTURAL PROTEIN / AUTOINHIBITION / ACTIN / NUCLEATION / CYTOSKELETON
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 / profilin binding / regulation of microtubule-based process / axon midline choice point recognition / 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 / small GTPase binding / ruffle membrane / spindle / neuron projection development / presynapse / actin binding / gene expression / regulation of cell shape / actin cytoskeleton organization / transmembrane transporter binding / positive regulation of cell migration / neuron projection / 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 / SAD / Resolution: 2.4 Å
AuthorsOtomo, T. / Otomo, C. / Tomchick, D.R. / Machius, M. / Rosen, M.K.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural Basis of Rho Gtpase-Mediated Activation of the Formin Mdia1
Authors: Otomo, T. / Otomo, C. / Tomchick, D.R. / Machius, M. / Rosen, M.K.
History
DepositionApr 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2263
Polymers89,1902
Non-polymers351
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-74.7 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.365, 121.365, 95.096
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein DIAPHANOUS PROTEIN HOMOLOG 1 / Transparency and translucency / DIAPHANOUS-RELATED FORMIN 1 / DRF1 / MDIA1 / P140MDIA


Mass: 44595.043 Da / Num. of mol.: 2 / Fragment: AMINO-TERMINAL DOMAIN, RESIDUES 131-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS TO GTP-BOUND FORM OF RHO AND TO PROFILIN. ACTS IN A RHO-DEPENDENT MANNER TO RECRUIT PROFILIN ...BINDS TO GTP-BOUND FORM OF RHO AND TO PROFILIN. ACTS IN A RHO-DEPENDENT MANNER TO RECRUIT PROFILIN TO THE MEMBRANE, WHERE IT PROMOTES ACTIN POLYMERIZATION. IT IS REQUIRED FOR CYTOKINESIS, STRESS FIBER FORMATION, AND TRANSCRIPTIONAL ACTIVATION OF THE SERUM RESPONSE FACTOR.

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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: 4.5 Å3/Da / Density % sol: 72.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.25
Details: HANGING DROP VAPOR DIFFUSION; PROTEIN: 11 MG/ML IN 100 MM HEPES, PH 7.25; RESERVOIR: 100 MM HEPES, PH 7.25, 9% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00691
DetectorType: CUSTOM / Detector: CCD / Date: Oct 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00691 Å / Relative weight: 1
ReflectionResolution: 2.4→46 Å / Num. obs: 61321 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 55.09 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.41 / SU ML: 0.136 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 470 THROUGH 474 IN CHAIN A WERE MODELED AS ALANINES. BECAUSE SEQUENCE ASSIGNMENT WAS AMBIGUOUS DUE TO THE WEAK ELECTRON DENSITY IN THIS REGION
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1542 2.5 %RANDOM
Rwork0.196 ---
obs0.197 59657 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å21.44 Å20 Å2
2--2.89 Å20 Å2
3----4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5403 0 1 249 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9737428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36225276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.369151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051542
X-RAY DIFFRACTIONr_chiral_restr0.1340.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024110
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.22586
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23801
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8761.53526
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42425474
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43732210
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7744.51954
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 107
Rwork0.269 4327
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1984-0.05130.20311.40691.26754.2677-0.0469-0.1299-0.0208-0.06730.1181-0.09140.37760.4327-0.0711-0.03550.0504-0.0098-0.04680.0133-0.10085.880161.950370.1327
21.5859-0.05490.19915.42660.35033.469-0.03320.07310.0171-0.57730.0224-0.1548-0.3220.10220.01070.10970.03630.0009-0.37110.0169-0.21465.686634.699738.8424
311.38670.834820.37385.91380.606344.0766-0.7347-0.6130.3401-0.77950.49120.648-0.8845-2.81880.2435-0.00780.0181-0.0261-0.00110.0404-0.0185-14.426436.808132.2589
41.0589-0.0095-0.21771.9869-1.17653.491-0.0346-0.16130.00230.02170.06930.0968-0.1881-0.3002-0.0346-0.14160.1011-0.0247-0.1483-0.0166-0.1314-0.4439.125260.3576
52.9331.15190.10424.7204-0.79331.7391-0.11250.1598-0.0746-0.63750.0708-0.2605-0.11110.07460.04170.14660.1129-0.0093-0.2715-0.0014-0.15086.249531.658138.3441
63.7688-0.79965.67417.0412-8.09122.2912-0.48710.1970.3059-1.0520.90011.13210.0855-1.3521-0.4130.19680.0222-0.3452-0.13460.12260.0704-12.242533.951328.9427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 380
2X-RAY DIFFRACTION2A381 - 444
3X-RAY DIFFRACTION3A445 - 474
4X-RAY DIFFRACTION4B133 - 370
5X-RAY DIFFRACTION5B371 - 444
6X-RAY DIFFRACTION6B445 - 477

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