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- PDB-3lxr: Shigella IpgB2 in complex with human RhoA and GDP (complex C) -

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Basic information

Entry
Database: PDB / ID: 3lxr
TitleShigella IpgB2 in complex with human RhoA and GDP (complex C)
Components
  • IpgB2
  • Transforming protein RhoA
KeywordsSignaling Protein/RHOA-BINDING PROTEIN / IpgB2 / RhoA / GTPase / GEF / GEF-GTPase-complex / WxxxE / TTSS effector protein / bacterial GEF / cytoskeleton dynamics / Signaling Protein-RHOA-BINDING PROTEIN complex
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway ...alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOA GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / RHO GTPases activate PKNs / GPVI-mediated activation cascade / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / secretory granule membrane / cell periphery / regulation of actin cytoskeleton organization / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium / cellular response to lipopolysaccharide / G alpha (12/13) signalling events / G protein activity / midbody / cell cortex / vesicle / dendritic spine / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / postsynapse / endosome / focal adhesion / GTPase activity / Neutrophil degranulation
Similarity search - Function
SopE-like GEF fold - #20 / Bacterial effector protein IpgB-like / IpaB/EvcA family / SopE-like GEF fold / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family ...SopE-like GEF fold - #20 / Bacterial effector protein IpgB-like / IpaB/EvcA family / SopE-like GEF fold / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA / IpgB2
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsKlink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of Shigella IPGB2 in complex with human RhoA: Implications for the mechanism of bacterial GEF-mimicry
Authors: Klink, B.U. / Barden, S. / Heidler, T.V. / Borchers, C. / Ladwein, M. / Stradal, T.E.B. / Rottner, K. / Heinz, D.W.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
F: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4156
Polymers42,6842
Non-polymers7314
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-9 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 100.790, 50.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transforming protein RhoA / H12


Mass: 20747.715 Da / Num. of mol.: 1 / Fragment: residues 2-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA / Plasmid: pET-28c / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: P61586
#2: Protein IpgB2 / IpgB2 / probably secreted by the Mxi-Spa secretion machinery


Mass: 21935.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgB2 / Plasmid: pET-M 41 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9AJW7
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350; post-crystallization treatment: EDTA, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.68→42.53 Å / Num. obs: 45588 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 23.76
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 4 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 12890 / Num. unique all: 3248 / Num. unique obs: 3248 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å42.55 Å
Translation1.98 Å42.55 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LWN

3lwn


Resolution: 1.68→42.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.859 / SU B: 4.495 / SU ML: 0.07 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.101 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2280 5 %RANDOM
Rwork0.17 ---
obs0.172 45585 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.02 Å2 / Biso mean: 17.277 Å2 / Biso min: 4.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.68→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 43 484 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223072
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.9784162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90124.662148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231522
X-RAY DIFFRACTIONr_chiral_restr0.1430.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212303
X-RAY DIFFRACTIONr_mcbond_it1.311.51849
X-RAY DIFFRACTIONr_mcangle_it2.26223018
X-RAY DIFFRACTIONr_scbond_it3.56431223
X-RAY DIFFRACTIONr_scangle_it5.6834.51135
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 163 -
Rwork0.246 3084 -
all-3247 -
obs--96.87 %
Refinement TLS params.

T11: 0.0712 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2666-0.14070.16450.57950.1290.3731-0.0109-0.0082-0.0176-0.0669-0.00030.0742-0.0147-0.0110.01120.0073-0.01790.08080.01460.079620.58111.3227.865
20.2485-0.03940.0530.5840.39810.3163-0.0401-0.0830.0630.02140.0606-0.02630.02860.0272-0.02050.0172-0.00360.0981-0.01010.078534.52823.70825.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 181
2X-RAY DIFFRACTION2F8 - 188

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