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- PDB-3dad: Crystal structure of the N-terminal regulatory domains of the for... -

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Basic information

Entry
Database: PDB / ID: 3dad
TitleCrystal structure of the N-terminal regulatory domains of the formin FHOD1
ComponentsFH1/FH2 domain-containing protein 1
KeywordsSIGNALING PROTEIN / Formin / FHOD1 / GTPase-binding domain / ubiquitin-superfold / armadillo repeats / Actin-binding / Coiled coil / Cytoplasm / Cytoskeleton / Phosphoprotein
Function / homology
Function and homology information


establishment of centrosome localization / bleb / regulation of stress fiber assembly / nuclear migration / cortical actin cytoskeleton organization / intercalated disc / positive regulation of stress fiber assembly / : / actin filament binding / cytoskeleton ...establishment of centrosome localization / bleb / regulation of stress fiber assembly / nuclear migration / cortical actin cytoskeleton organization / intercalated disc / positive regulation of stress fiber assembly / : / actin filament binding / cytoskeleton / protein domain specific binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FHOD1, N-terminal GTPase-binding domain / Formin N-terminal 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 ...FHOD1, N-terminal GTPase-binding domain / Formin N-terminal 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
FH1/FH2 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSchulte, A. / Stolp, B. / Schonichen, A. / Pylypenko, O. / Rak, A. / Fackler, O.T. / Geyer, M.
Citation
Journal: Structure / Year: 2008
Title: The Human Formin FHOD1 Contains a Bipartite Structure of FH3 and GTPase-Binding Domains Required for Activation.
Authors: Schulte, A. / Stolp, B. / Schonichen, A. / Pylypenko, O. / Rak, A. / Fackler, O.T. / Geyer, M.
#1: Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun / Year: 2007
Title: Purification, crystallization and preliminary structural characterization of the N-terminal region of the human formin-homology protein FHOD1.
Authors: Schulte, A. / Rak, A. / Pylypenko, O. / Ludwig, D. / Geyer, M.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 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: FH1/FH2 domain-containing protein 1
B: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)74,5472
Polymers74,5472
Non-polymers00
Water4,288238
1
A: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)37,2731
Polymers37,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)37,2731
Polymers37,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.444, 73.931, 78.674
Angle α, β, γ (deg.)78.24, 86.17, 89.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein FH1/FH2 domain-containing protein 1 / Formin homolog overexpressed in spleen 1 / FHOS / Formin homology 2 domain-containing protein 1


Mass: 37273.266 Da / Num. of mol.: 2 / Fragment: GBD and FH3 domain / Mutation: C31S, C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FHOD1, FHOS, FHOS1 / Plasmid: pProEx-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9Y613
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97883 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.3→19.687 Å / Num. all: 32912 / Num. obs: 32912

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementResolution: 2.3→19.6 Å / Cross valid method: THROUGHOUT / σ(I): 3.8
RfactorNum. reflection% reflectionSelection details
Rfree0.259 --random
Rwork0.219 ---
all-34699 --
obs-32912 94.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 0 238 5072

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