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- PDB-1by1: DBL homology domain from beta-PIX -

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Basic information

Entry
Database: PDB / ID: 1by1
TitleDBL homology domain from beta-PIX
ComponentsPROTEIN (PIX)
KeywordsTRANSPORT PROTEIN / RHO-GTPASE EXCHANGE FACTOR
Function / homology
Function and homology information


negative regulation of microtubule nucleation / positive regulation of lamellipodium morphogenesis / focal adhesion assembly / gamma-tubulin binding / positive regulation of fibroblast migration / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / Activation of RAC1 downstream of NMDARs / NRAGE signals death through JNK ...negative regulation of microtubule nucleation / positive regulation of lamellipodium morphogenesis / focal adhesion assembly / gamma-tubulin binding / positive regulation of fibroblast migration / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / Activation of RAC1 downstream of NMDARs / NRAGE signals death through JNK / mitotic spindle pole / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / ephrin receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / ruffle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / EGFR downregulation / positive regulation of GTPase activity / G alpha (12/13) signalling events / lamellipodium / nervous system development / cell cortex / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / protein kinase binding / signal transduction / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain ...Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsAghazadeh, B. / Zhu, K. / Kubiseski, T.J. / Liu, G.A. / Pawson, T. / Zheng, Y. / Rosen, M.K.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure and Mutagenesis of the Dbl Homology Domain
Authors: Aghazadeh, B. / Zhu, K. / Kubiseski, T.J. / Liu, G.A. / Pawson, T. / Zheng, Y. / Rosen, M.K.
History
DepositionOct 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (PIX)


Theoretical massNumber of molelcules
Total (without water)23,9721
Polymers23,9721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (PIX)


Mass: 23972.473 Da / Num. of mol.: 1 / Fragment: DBL HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14155

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY TOCSY 2D
121NOESY TOCSY 3D THROUGH BOND TRANSFER EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF TRIPLE- AND QUADRUPLE- RESONANCE NMR EXPERIMENTS ON 13C/ 15N AND PARTIALLY OR FULLY DEUTERATED SAMPLES WITH SELECTIVE METHYL LABELING AT ...Text: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF TRIPLE- AND QUADRUPLE- RESONANCE NMR EXPERIMENTS ON 13C/ 15N AND PARTIALLY OR FULLY DEUTERATED SAMPLES WITH SELECTIVE METHYL LABELING AT VALINE,LEUCINE AND ISOLEUCINES.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM / pH: 7.0 / Pressure: 1 atm / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY INOVA / Manufacturer: Varian / Model: UNITY INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS 0.3, X-PLOR3.851A.BRUNGER, M.NILGESrefinement
NMRPipestructure solution
NMRViewstructure solution
ARIAstructure solution
X-PLORstructure solution
CNSstructure solution
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: X-PLOR 3.851 WAS USED IN COMBINATION WITH ARIA (REF. M. NILGES)
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 80 / Conformers submitted total number: 20

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