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- PDB-1htj: STRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF -

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Basic information

Entry
Database: PDB / ID: 1htj
TitleSTRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF
ComponentsKIAA0380
KeywordsSIGNALING PROTEIN / RGS-like / Regulator of G protein signaling / GEF / Guanine nucleotide exchange factor
Function / homology
Function and homology information


Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction ...Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / regulation of cell growth / G alpha (12/13) signalling events / actin cytoskeleton organization / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / RGS domain ...Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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 profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLongenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2001
Title: Structure of the RGS-like domain from PDZ-RhoGEF: linking heterotrimeric g protein-coupled signaling to Rho GTPases.
Authors: Longenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S.
History
DepositionDec 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: KIAA0380


Theoretical massNumber of molelcules
Total (without water)23,9011
Polymers23,9011
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.61, 61.61, 201.91
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe assymetric unit contains a protein fragment that is a single domain isolated from a multi-domain protein, and is not known to organize into multimers.

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Components

#1: Protein KIAA0380


Mass: 23901.242 Da / Num. of mol.: 1 / Fragment: RGS-LIKE DOMAIN (RESIDUES 281-490) / Mutation: K463A, E465A, E466A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0380 / Plasmid details: BASED ON PET22B / Plasmid: PHIS-PARALLEL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O15085
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.3 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium Sulfate, PEG 400, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mMdithiothreitol1drop
440-42 %satammonium sulfate1reservoir
52 %PEG4001reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9717 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 12161 / Num. obs: 12161 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1160 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 57934
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
SOLVEphasing
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 799 6.5 %RANDOM
Rwork0.223 ---
obs0.226 11167 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.212 Å2-8.331 Å20 Å2
2---10.212 Å20 Å2
3---20.423 Å2
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.35 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 84 1529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.257
X-RAY DIFFRACTIONc_dihedral_angle_d19.34
X-RAY DIFFRACTIONc_improper_angle_d0.7427
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.381 69 -
Rwork0.36 820 -
obs-889 76 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 6.5 % / Rfactor all: 0.226 / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.34
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7427
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / Rfactor Rwork: 0.36

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