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- PDB-3eg5: Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP -

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Basic information

Entry
Database: PDB / ID: 3eg5
TitleCrystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP
Components
  • Cell division control protein 42 homolog
  • Protein diaphanous homolog 1
KeywordsSIGNALING PROTEIN / PROTEIN-PROTEIN COMPLEX / RHO PROTEINS / DIAPHANOUS / FORMINS / ARMADILLO REPEAT / G-PROTEIN / GTPASE / Alternative splicing / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation / Actin-binding / Cell projection / Coiled coil / Cytoplasm / Cytoskeleton / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


RHO GTPases activate KTN1 / RHOV GTPase cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / DCC mediated attractive signaling / RHOF GTPase cycle / CD28 dependent Vav1 pathway / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle ...RHO GTPases activate KTN1 / RHOV GTPase cycle / negative regulation of neuron projection regeneration / multicellular organismal locomotion / DCC mediated attractive signaling / RHOF GTPase cycle / CD28 dependent Vav1 pathway / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / RHOB GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate PAKs / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / establishment or maintenance of apical/basal cell polarity / CDC42 GTPase cycle / RHOD GTPase cycle / G beta:gamma signalling through CDC42 / GPVI-mediated activation cascade / RHOA GTPase cycle / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / EGFR downregulation / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / Golgi transport complex / RHOG GTPase cycle / actin nucleation / positive regulation of pinocytosis / neuron projection retraction / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / RHO GTPases activate IQGAPs / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / RHO GTPases Activate Formins / neuron fate determination / protein localization to microtubule / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / profilin binding / positive regulation of pseudopodium assembly / Regulation of actin dynamics for phagocytic cup formation / MAPK6/MAPK4 signaling / cellular response to histamine / cardiac conduction system development / heart process / Factors involved in megakaryocyte development and platelet production / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / Myogenesis / nucleus localization / cell junction assembly / filopodium assembly / regulation of microtubule-based process / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / regulation of release of sequestered calcium ion into cytosol / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / VEGFA-VEGFR2 Pathway / regulation of stress fiber assembly / regulation of lamellipodium assembly / axon midline choice point recognition / nuclear migration / adherens junction organization / sprouting angiogenesis / regulation of postsynapse organization / positive regulation of filopodium assembly / endosomal transport / regulation of cytoskeleton organization / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / heart contraction / Golgi organization / positive regulation of cytokinesis / cell leading edge / brush border / lamellipodium membrane / Rho protein signal transduction / synaptic vesicle endocytosis / ephrin receptor signaling pathway / spindle midzone / positive regulation of DNA replication
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 / Cdc42 / 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 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLammers, M. / Meyer, S. / Kuehlmann, D. / Wittinghofer, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Specificity of Interactions between mDia Isoforms and Rho Proteins
Authors: Lammers, M. / Meyer, S. / Kuhlmann, D. / Wittinghofer, A.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 42 homolog
B: Protein diaphanous homolog 1
C: Cell division control protein 42 homolog
D: Protein diaphanous homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1008
Polymers128,0074
Non-polymers1,0934
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.269, 71.269, 244.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA1 - 1781 - 178
21METMETGLUGLUCC1 - 1781 - 178
12VALVALHISHISBB83 - 43515 - 367
22VALVALHISHISDD83 - 43515 - 367

NCS ensembles :
ID
1
2

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Components

#1: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 19802.719 Da / Num. of mol.: 2 / Fragment: UNP residues 1-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: MUS MUSCULUSHouse mouse / Gene: Cdc42 / Plasmid: CDC42-1-178-PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60766
#2: Protein Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1 / p140mDIA / mDIA1


Mass: 44200.680 Da / Num. of mol.: 2 / Fragment: MDIAN-TSH, UNP residues 69-451 / Mutation: N164T, N165S, N166H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: MUS MUSCULUSHouse mouse / Gene: Diaph1 / Plasmid: MDIAN-TSH-PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→43.478 Å / Num. all: 38241 / Num. obs: 38038 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Rsym value: 0.084 / Net I/σ(I): 13.52
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.69 / Rsym value: 0.333 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z2C

1z2c


Resolution: 2.7→43.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.101 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.986 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24333 1908 5 %RANDOM
Rwork0.20629 ---
obs0.20816 36130 99.49 %-
all-38038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8228 0 66 47 8341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.99811400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02351022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53624.922386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.867151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0341552
X-RAY DIFFRACTIONr_chiral_restr0.0720.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23859
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25858
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3471.55298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59828360
X-RAY DIFFRACTIONr_scbond_it0.82833467
X-RAY DIFFRACTIONr_scangle_it1.4114.53040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1391tight positional0.010.05
2B2723tight positional0.010.05
1A1391tight thermal0.020.5
2B2723tight thermal0.020.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 125 -
Rwork0.287 2693 -
obs--99.86 %

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