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- PDB-5efx: Crystal structure of Rho GTPase regulator -

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Basic information

Entry
Database: PDB / ID: 5efx
TitleCrystal structure of Rho GTPase regulator
ComponentsRho guanine nucleotide exchange factor 2
KeywordsSIGNALING PROTEIN / Rho GTPase / activity
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / cellular hyperosmotic response / negative regulation of necroptotic process / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / cellular hyperosmotic response / negative regulation of necroptotic process / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOA GTPase cycle / bicellular tight junction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of neuron differentiation / guanyl-nucleotide exchange factor activity / actin filament organization / intracellular protein transport / cell morphogenesis / spindle / ruffle membrane / small GTPase binding / positive regulation of interleukin-6 production / G alpha (12/13) signalling events / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / cytoplasmic vesicle / microtubule binding / vesicle / microtubule / cytoskeleton / cell cycle / focal adhesion / innate immune response / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
ARHGEF2, PH domain / ARHGEF1-like, PH domain / 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...ARHGEF2, PH domain / ARHGEF1-like, PH domain / 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsJiang, Y. / Ouyang, S. / Liu, Z.J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of hGEF-H1 PH domain provides insight into incapability in phosphoinositide binding
Authors: Jiang, Y. / Jiang, H. / Zhou, S. / Meng, B. / Liu, Z.J. / Ouyang, S.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 2


Theoretical massNumber of molelcules
Total (without water)16,6041
Polymers16,6041
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7760 Å2
Unit cell
Length a, b, c (Å)37.948, 81.825, 119.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

#1: Protein Rho guanine nucleotide exchange factor 2 / Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell ...Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell nucleolar antigen p40


Mass: 16604.268 Da / Num. of mol.: 1 / Fragment: UNP residues 439-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q92974
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.07 % / Description: cubic crystals, very beautiful
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Sodium Nitrate, 20% PEG 3350, PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 7006 / % possible obs: 97.2 % / Redundancy: 12.5 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 60.5
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 8.29 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data processing
Cootmodel building
PHASERphasing
Cootrefinement
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0N

4d0n


Resolution: 2.451→36.177 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 330 4.71 %Random selection
Rwork0.2172 ---
obs0.2188 7003 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 2.451→36.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 0 30 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091189
X-RAY DIFFRACTIONf_angle_d1.2131609
X-RAY DIFFRACTIONf_dihedral_angle_d15.03463
X-RAY DIFFRACTIONf_chiral_restr0.078181
X-RAY DIFFRACTIONf_plane_restr0.005208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4505-3.08720.30791800.26613165X-RAY DIFFRACTION94
3.0872-36.18120.23151500.20353508X-RAY DIFFRACTION100

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