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- PDB-3lwn: Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex B) -

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Basic information

Entry
Database: PDB / ID: 3lwn
TitleShigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex B)
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 / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / regulation of osteoblast proliferation ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / regulation of osteoblast proliferation / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / establishment of epithelial cell apical/basal polarity / beta selection / negative regulation of cell size / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / odontogenesis / PCP/CE pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / positive regulation of cytokinesis / regulation of neuron projection development / RHOC GTPase cycle / cellular response to cytokine stimulus / androgen receptor signaling pathway / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / mitotic spindle assembly / endothelial cell migration / RHOA GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / skeletal muscle tissue development / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / kidney development / secretory granule membrane / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / G protein activity / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events
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 family 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 family 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Transforming protein RhoA
F: IpgB2
G: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3028
Polymers85,3674
Non-polymers9354
Water7,837435
1
A: Transforming protein RhoA
F: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1514
Polymers42,6842
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-8 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: Transforming protein RhoA
G: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1514
Polymers42,6842
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-7 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.530, 95.700, 102.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transforming protein RhoA / H12


Mass: 20747.715 Da / Num. of mol.: 2 / 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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350; protein was treated with EDTA prior to crystallization, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 6, 2009
RadiationMonochromator: RIGAKU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→35.13 Å / Num. obs: 34100 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 9.81
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 7665 / Num. unique all: 2183 / Num. unique obs: 2183 / % possible all: 86.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å35.13 Å
Translation2.4 Å35.13 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LW8

3lw8


Resolution: 2.28→35.13 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 20.323 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.459 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1705 5 %RANDOM
Rwork0.204 ---
obs0.209 34099 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.57 Å2 / Biso mean: 16.746 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.28→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5770 0 58 435 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226064
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9738202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77624.88291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.564151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0121539
X-RAY DIFFRACTIONr_chiral_restr0.1110.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214529
X-RAY DIFFRACTIONr_mcbond_it0.71.53664
X-RAY DIFFRACTIONr_mcangle_it1.27525970
X-RAY DIFFRACTIONr_scbond_it2.25532400
X-RAY DIFFRACTIONr_scangle_it3.4954.52214
LS refinement shellResolution: 2.283→2.342 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 108 -
Rwork0.252 2065 -
all-2173 -
obs--86.26 %
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)
11.4199-0.07160.35261.96870.59241.62020.0512-0.0366-0.0145-0.1616-0.08040.0586-0.0489-0.16880.02930.02290.0045-0.01190.0819-0.00680.01990.5588.5938.16
21.7119-0.16980.47451.82990.05311.46320.0666-0.0101-0.0533-0.0804-0.02650.00370.0868-0.0328-0.04020.0234-0.0221-0.00410.03510.00730.02390.51611.91959.791
31.581-0.6288-0.0292.45320.40891.9449-0.0242-0.10670.07850.04570.0262-0.1333-0.08580.1007-0.0020.0454-0.0383-0.01920.0907-0.00790.075715.27220.64125.071
41.104-0.61260.06492.48340.06472.0233-0.0546-0.14130.13330.13260.0748-0.1104-0.01820.1544-0.02020.0444-0.046-0.01870.1126-0.03210.099215.25623.91276.843
50.1505-0.0578-0.01780.11320.08130.62530.0212-0.01050.0152-0.005-0.0174-0.0033-0.02040.0342-0.00390.1217-0.0291-0.02340.11260.0060.1627.18115.87239.061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2B1 - 181
3X-RAY DIFFRACTION3F8 - 188
4X-RAY DIFFRACTION4G8 - 188
5X-RAY DIFFRACTION5A302 - 442
6X-RAY DIFFRACTION5B303 - 451
7X-RAY DIFFRACTION5G189 - 452
8X-RAY DIFFRACTION5F189 - 440

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