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- PDB-1z2c: Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP -

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Basic information

Entry
Database: PDB / ID: 1z2c
TitleCrystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP
Components
  • Diaphanous protein homolog 1Transparency and translucency
  • Rho-related GTP-binding protein RhoC
KeywordsSIGNALING PROTEIN / armadillo repeat
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 / positive regulation of lipase activity / skeletal muscle satellite cell migration / profilin binding / RHO GTPases Activate Rhotekin and Rhophilins / cellular response to histamine / stereocilium / apical junction assembly / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / axon midline choice point recognition / wound healing, spreading of cells / regulation of cytoskeleton organization / small GTPase-mediated signal transduction / RHOC GTPase cycle / cleavage furrow / brush border / mitotic cytokinesis / synaptic vesicle endocytosis / ephrin receptor signaling pathway / cytoskeleton organization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / actin filament polymerization / Neutrophil degranulation / actin filament organization / actin filament / RHO GTPases Activate Formins / positive regulation of protein-containing complex assembly / sensory perception of sound / brain development / protein localization / mitotic spindle / ruffle membrane / small GTPase binding / neuron projection development / G alpha (12/13) signalling events / presynapse / gene expression / actin binding / regulation of cell shape / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / neuron projection / positive regulation of cell migration / GTPase activity / centrosome / GTP binding / endoplasmic reticulum membrane / protein kinase binding / signal transduction / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Formin, diaphanous GTPase-binding 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 ...Formin, diaphanous GTPase-binding 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 / Small GTPase Rho / small GTPase Rho family profile. / Histone, subunit A / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Recoverin; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein diaphanous homolog 1 / Rho-related GTP-binding protein RhoC
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsRose, R. / Weyand, M. / Lammers, M. / Ishizaki, T. / Ahmadian, M.R. / Wittinghofer, A.
Citation
Journal: Nature / Year: 2005
Title: Structural and mechanistic insights into the interaction between Rho and mammalian Dia.
Authors: Rose, R. / Weyand, M. / Lammers, M. / Ishizaki, T. / Ahmadian, M.R. / Wittinghofer, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The purification and crystallisation of mDia1 in complex with RhoC
Authors: Rose, R. / Wittinghofer, A. / Weyand, M.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoC
B: Diaphanous protein homolog 1
C: Rho-related GTP-binding protein RhoC
D: Diaphanous protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5619
Polymers132,4444
Non-polymers1,1175
Water0
1
A: Rho-related GTP-binding protein RhoC
B: Diaphanous protein homolog 1
hetero molecules

A: Rho-related GTP-binding protein RhoC
B: Diaphanous protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,58610
Polymers132,4444
Non-polymers1,1426
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
2
C: Rho-related GTP-binding protein RhoC
D: Diaphanous protein homolog 1
hetero molecules

C: Rho-related GTP-binding protein RhoC
D: Diaphanous protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5378
Polymers132,4444
Non-polymers1,0934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)148.640, 85.350, 123.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer generated from chains A and B in the asymmetric unit by the operations: -0.5566*x+ 0.8306*y+ 0.0185*z+ 45.4814 0.8139*x+ 0.5407*y+ 0.2125*z+ -31.7436 0.1665*x+ 0.1333*y+ -0.9770*z+ 34.8241 / The biological assembly is a tetramer generated from chains C and D in the asymmetric unit by the operations: -0.5566*x+ 0.8139*y+ 0.1665*z+ 45.3525 0.8306*x+ 0.5407*y+ 0.1333*z+ -25.2564 0.0185*x+ 0.2125*y+ -0.9770*z+ 39.9275

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Components

#1: Protein Rho-related GTP-binding protein RhoC / H9 / RhoC


Mass: 22005.320 Da / Num. of mol.: 2 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOC, ARH9, ARHC / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08134
#2: Protein Diaphanous protein homolog 1 / Transparency and translucency / Diaphanous-related formin 1 / DRF1 / mDIA1 / p140mDIA


Mass: 44216.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Diaph1, Diap1 / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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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: 3.1 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 2000-MME, magnesium sulphate, Tris buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 31996 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.06 %
Reflection shellResolution: 3→3.1 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.867 / SU B: 44.926 / SU ML: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28515 1605 5 %RANDOM
Rwork0.21057 ---
all0.21436 30390 --
obs0.21436 30390 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 67 0 8399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.99511522
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58351031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31624.879414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.013151639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6581563
X-RAY DIFFRACTIONr_chiral_restr0.1080.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026314
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.23886
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25827
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1320.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5871.55339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01328398
X-RAY DIFFRACTIONr_scbond_it1.51533550
X-RAY DIFFRACTIONr_scangle_it2.534.53124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 117 -
Rwork0.336 2149 -
obs--100 %
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)
14.31691.2128-0.56432.81650.37466.20970.1123-0.306-0.6470.26150.02730.01010.9522-0.3054-0.1396-0.1938-0.1352-0.1612-0.14810.0432-0.150917.168676.998687.2445
20.27020.37810.68052.23182.56693.8433-0.08530.15250.0709-0.25640.04620.149-0.2983-0.08750.0391-0.2269-0.01930.0238-0.21640.0729-0.191527.4522108.743103.6453
33.06711.57970.01084.4510.32815.3697-0.18270.5944-0.1519-0.6819-0.0072-0.4594-0.25840.24850.19-0.14740.0884-0.0251-0.0646-0.2069-0.112216.313173.135746.3686
42.2231.1262.56310.9411.8023.64290.0478-0.05080.1289-0.06220.0795-0.1191-0.14580.2815-0.1273-0.1856-0.04040.0254-0.1889-0.0083-0.0795-13.962754.744832.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1791 - 179
2X-RAY DIFFRACTION2BB83 - 44315 - 375
3X-RAY DIFFRACTION3CC1 - 1791 - 179
4X-RAY DIFFRACTION4DD83 - 43615 - 368

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