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- PDB-3odo: Crystal Structure of the DH/PH Domains of p115-RhoGEF -

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Basic information

Entry
Database: PDB / ID: 3odo
TitleCrystal Structure of the DH/PH Domains of p115-RhoGEF
ComponentsRho guanine nucleotide exchange factor 1
KeywordsSIGNALING PROTEIN / regulation of RhoA GTPase / RhoGEF / DH / PH / Rho
Function / homology
Function and homology information


regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events ...regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events / G protein-coupled receptor signaling pathway / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / RGS domain superfamily / Dbl homology (DH) domain superfamily ...p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, Z. / Guo, L. / Sprang, S.R. / Sternweis, P.C.
CitationJournal: Protein Sci. / Year: 2011
Title: Modulation of a GEF switch: Autoinhibition of the intrinsic guanine nucleotide exchange activity of p115-RhoREF
Authors: Chen, Z. / Guo, L. / Sprang, S.R. / Sternweis, P.C.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
B: Rho guanine nucleotide exchange factor 1


Theoretical massNumber of molelcules
Total (without water)87,5392
Polymers87,5392
Non-polymers00
Water0
1
A: Rho guanine nucleotide exchange factor 1


Theoretical massNumber of molelcules
Total (without water)43,7701
Polymers43,7701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho guanine nucleotide exchange factor 1


Theoretical massNumber of molelcules
Total (without water)43,7701
Polymers43,7701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.049, 106.049, 125.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Rho guanine nucleotide exchange factor 1 / 115 kDa guanine nucleotide exchange factor / p115-RhoGEF / p115RhoGEF / Sub1.5


Mass: 43769.539 Da / Num. of mol.: 2 / Fragment: DH-PH domain RESIDUES 395-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF1 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92888

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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: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.6-2.8M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2010 / Details: Mirrors
RadiationMonochromator: Double-crystal Si-111 & Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 30747 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X86

1x86


Resolution: 2.9→36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 47.33 / SU ML: 0.371 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1550 5 %RANDOM
Rwork0.221 ---
obs0.223 29151 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.613 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2--5.98 Å20 Å2
3----11.97 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 0 0 6068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226183
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.988351
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72823.377302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.356151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221564
X-RAY DIFFRACTIONr_chiral_restr0.120.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4931.53716
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98726037
X-RAY DIFFRACTIONr_scbond_it1.76832467
X-RAY DIFFRACTIONr_scangle_it3.0454.52314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3028 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.290.5
medium thermal0.422
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 110 -
Rwork0.372 2130 -
obs--98.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29810.72873.20742.91841.002812.1177-0.14650.29810.2725-0.1875-0.0299-0.167-1.19241.77190.17640.4653-0.15950.01960.4313-0.0320.413750.9418-37.477925.7482
28.789-3.4360.1927.6833-1.42634.7786-0.46840.26390.11660.89890.0735-0.15810.3166-0.01830.39490.8312-0.1631-0.05220.05680.00370.288124.0621-11.57181.4429
32.4557-0.64173.09962.8164-1.216511.8089-0.1002-0.35070.34280.1601-0.07240.1911-1.0785-1.80590.17270.44420.18340.01560.41820.00440.4322.093615.559-17.893
48.91243.3764-0.6167.58591.58814.8347-0.5108-0.4440.0661-0.90930.17160.13930.28710.10490.33920.82960.1657-0.06730.0901-0.00420.298628.964741.45376.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A392 - 609
2X-RAY DIFFRACTION2A610 - 761
3X-RAY DIFFRACTION3B392 - 609
4X-RAY DIFFRACTION4B610 - 761

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