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- PDB-3lw8: Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) -

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Basic information

Entry
Database: PDB / ID: 3lw8
TitleShigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A)
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 / SLIT2:ROBO1 increases RHOA activity ...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 / 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 / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / regulation of modification of postsynaptic structure / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / cellular response to chemokine / beta selection / negative regulation of oxidative phosphorylation / regulation of systemic arterial blood pressure by endothelin / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / androgen receptor signaling pathway / stress fiber assembly / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / skeletal muscle tissue development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / Rho protein signal transduction / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of cell migration / regulation of microtubule cytoskeleton organization / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / VEGFA-VEGFR2 Pathway / cytoplasmic side of plasma membrane / ruffle membrane / neuron migration / cell morphogenesis / Ovarian tumor domain proteases / cell junction / G beta:gamma signalling through PI3Kgamma
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: 1.85 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 23, 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 / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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.ptnr1_label_seq_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
C: Transforming protein RhoA
D: Transforming protein RhoA
E: IpgB2
F: IpgB2
G: IpgB2
H: IpgB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,60516
Polymers170,7358
Non-polymers1,8708
Water31,8141766
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 area2170 Å2
ΔGint-6 kcal/mol
Surface area18530 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 area2530 Å2
ΔGint-8 kcal/mol
Surface area18450 Å2
MethodPISA
3
C: Transforming protein RhoA
H: 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 area2500 Å2
ΔGint-5 kcal/mol
Surface area18520 Å2
MethodPISA
4
D: Transforming protein RhoA
E: 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 area2580 Å2
ΔGint-6 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.590, 101.600, 97.030
Angle α, β, γ (deg.)90.000, 96.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transforming protein RhoA / H12


Mass: 20747.715 Da / Num. of mol.: 4 / 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.: 4
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1766 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350, 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: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.85→48.21 Å / Num. obs: 133487 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.11
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 25173 / Num. unique all: 9777 / Num. unique obs: 9777 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S1C, partially refined structure of free IpgB2

1s1c


Resolution: 1.85→48.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.842 / SU B: 7.155 / SU ML: 0.103 / SU R Cruickshank DPI: 0.148 / SU Rfree: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6674 5 %RANDOM
Rwork0.177 ---
obs0.18 133481 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 109.74 Å2 / Biso mean: 21.609 Å2 / Biso min: 4.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.29 Å2
2--1.47 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11613 0 116 1766 13495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212362
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.97816731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21751562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97324.778586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15152397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9791585
X-RAY DIFFRACTIONr_chiral_restr0.1010.21846
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219237
X-RAY DIFFRACTIONr_mcbond_it0.7771.57479
X-RAY DIFFRACTIONr_mcangle_it1.361212205
X-RAY DIFFRACTIONr_scbond_it2.15334883
X-RAY DIFFRACTIONr_scangle_it3.454.54480
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 487 -
Rwork0.263 9262 -
all-9749 -
obs--97.74 %
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)
10.911-0.4133-0.26530.96120.25821.1603-0.02960.0022-0.1513-0.045-0.00480.09970.137-0.14620.03450.0569-0.0214-0.01830.04260.01690.0942-4.4317.57455.834
21.39490.5448-0.74190.9215-0.58322.17940.0051-0.1060.0779-0.1235-0.04350.0336-0.1570.21340.03850.0824-0.00970.01270.0995-0.01380.030234.711-0.8896.636
30.9321-0.28540.12761.0643-0.34831.0506-0.0298-0.03090.1426-0.0572-0.0162-0.1139-0.11120.08650.04610.073-0.01890.01470.0391-0.0120.082634.72-0.46255.901
41.0936-0.00850.31211.27510.40251.72010.0772-0.0133-0.125-0.1461-0.0773-0.01590.1997-0.14220.00010.0598-0.0334-0.00930.14770.04630.032-3.93517.4836.329
50.7204-0.33410.64441.36070.4222.55420.0084-0.02190.10880.0885-0.0390.0247-0.08590.04250.03060.0365-0.02660.02430.1036-0.00060.07051.47336.21833.042
61.767-0.23620.06490.65010.12160.7090.03720.1568-0.0075-0.0604-0.0199-0.0780.0336-0.0194-0.01720.0851-0.02050.00970.1096-0.00690.068812.30728.58221.459
70.5052-0.52050.33582.99090.06551.6972-0.2119-0.29760.14540.10650.3221-0.2459-0.12740.0941-0.11020.09330.1245-0.06160.2583-0.11510.07641.32338.280.781
81.8483-0.73440.06020.59370.10370.7419-0.0079-0.2714-0.0361-0.00880.0957-0.06630.00950.0789-0.08790.063-0.0089-0.01020.08780.00250.106912.44430.15769.132
90.2879-0.2215-0.36141.3407-0.41982.53770.0234-0.0316-0.10210.0342-0.01420.1110.121-0.033-0.00930.0289-0.0189-0.00730.09540.00920.076428.691-19.70132.891
101.3515-0.1731-0.08230.745-0.08650.97230.03370.11730.0588-0.0835-0.06530.03470.0242-0.08620.03160.0836-0.00960.0110.09660.02370.057518.83-11.57621.988
111.0089-0.3432-0.49062.672-0.14553.0085-0.1331-0.0856-0.01540.04240.10730.14170.0741-0.01290.02580.07330.01560.01640.1150.04990.100329.468-23.91480.321
121.4057-0.41570.04110.667-0.08580.8413-0.0395-0.09730.05560.0230.0380.0644-0.0707-0.10340.00150.09650.00180.01250.07380.00790.081718.685-12.03370.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 181
2X-RAY DIFFRACTION2B-3 - 179
3X-RAY DIFFRACTION3C-3 - 181
4X-RAY DIFFRACTION4D2 - 181
5X-RAY DIFFRACTION5E12 - 70
6X-RAY DIFFRACTION6E71 - 188
7X-RAY DIFFRACTION7F12 - 69
8X-RAY DIFFRACTION8F70 - 188
9X-RAY DIFFRACTION9G12 - 71
10X-RAY DIFFRACTION10G72 - 188
11X-RAY DIFFRACTION11H13 - 61
12X-RAY DIFFRACTION12H62 - 188

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