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- PDB-2dx1: Crystal structure of RhoGEF protein Asef -

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Basic information

Entry
Database: PDB / ID: 2dx1
TitleCrystal structure of RhoGEF protein Asef
ComponentsRho guanine nucleotide exchange factor 4
KeywordsSIGNALING PROTEIN / Rho-GEF / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


filopodium assembly / regulation of small GTPase mediated signal transduction / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / ruffle membrane / G alpha (12/13) signalling events ...filopodium assembly / regulation of small GTPase mediated signal transduction / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / ruffle membrane / G alpha (12/13) signalling events / intracellular signal transduction / protein domain specific binding / cytosol
Similarity search - Function
Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. ...Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.36 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism
Authors: Murayama, K. / Shirouzu, M. / Kawasaki, Y. / Kato-Murayama, M. / Hanawa-Suetsugu, K. / Sakamoto, A. / Katsura, Y. / Suenaga, A. / Toyama, M. / Terada, T. / Taiji, M. / Akiyama, T. / Yokoyama, S.
History
DepositionAug 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)55,6241
Polymers55,6241
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.932, 79.818, 68.004
Angle α, β, γ (deg.)90.00, 123.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rho guanine nucleotide exchange factor 4 / APC-stimulated guanine nucleotide exchange factor / Asef


Mass: 55623.777 Da / Num. of mol.: 1 / Fragment: residues 59-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PX041202-06-MD01 / Production host: CELL FREE PROTEIN SYNTHESIS (others) / References: UniProt: Q9NR80
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CORRECT SEQUENCE DATABASE IS Q9NR80-3(ISOFORM 3).

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2M MgCl2, 0.1M HEPES-HCl buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9789, 0.9794, 0.9640
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97941
30.9641
ReflectionResolution: 2.36→50 Å / Num. obs: 18703 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Biso Wilson estimate: 36.2 Å2
Reflection shellResolution: 2.36→2.44 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.36→34.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1381375.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1834 9.8 %RANDOM
Rwork0.232 ---
obs-18635 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.643 Å2 / ksol: 0.322373 e/Å3
Displacement parametersBiso mean: 53.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.98 Å20 Å26.4 Å2
2---1.65 Å20 Å2
3----6.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.36→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 0 64 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it3.991.5
X-RAY DIFFRACTIONc_mcangle_it5.672
X-RAY DIFFRACTIONc_scbond_it6.192
X-RAY DIFFRACTIONc_scangle_it7.742.5
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 309 10 %
Rwork0.325 2779 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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