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- PDB-3rf3: Shigella IpaA-VBS3 in complex with human vinculin -

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Basic information

Entry
Database: PDB / ID: 3rf3
TitleShigella IpaA-VBS3 in complex with human vinculin
Components
  • Invasin ipaA
  • Vinculin
Keywordsprotein binding/toxin / alpha-helix bundle domain / cytoskeletal protein / protein-protein interactions / cell adhesion / cytoskeleton / bacterial toxins / pathogen-host interactions / IpaA / Talin / F-actin / phosphatidylinositol 4 5-bisphosphate / Cytosol / Focal adhesion / protein binding-toxin complex
Function / homology
Function and homology information


positive regulation of actin filament depolymerization / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding ...positive regulation of actin filament depolymerization / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / specific granule lumen / extracellular vesicle / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SipA, vinculin binding site / SipA vinculin binding site / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. ...SipA, vinculin binding site / SipA vinculin binding site / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / Invasin IpaA / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsPark, H. / Sharff, A. / Izard, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Novel vinculin binding site of the IpaA invasin of Shigella.
Authors: Park, H. / Valencia-Gallardo, C. / Sharff, A. / Tran Van Nhieu, G. / Izard, T.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Sep 13, 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: Vinculin
B: Vinculin
C: Invasin ipaA
D: Invasin ipaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4286
Polymers64,1544
Non-polymers2742
Water14,484804
1
A: Vinculin
C: Invasin ipaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2143
Polymers32,0772
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-22 kcal/mol
Surface area14790 Å2
MethodPISA
2
B: Vinculin
D: Invasin ipaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2143
Polymers32,0772
Non-polymers1371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-22 kcal/mol
Surface area15000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-39 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.583, 85.319, 137.904
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 Vinculin / / Metavinculin


Mass: 28937.398 Da / Num. of mol.: 2 / Fragment: unp residues 1-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL, vinculin / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18206
#2: Protein/peptide Invasin ipaA / 70 kDa antigen


Mass: 3139.582 Da / Num. of mol.: 2 / Fragment: unp residues 488-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: CP0125, ipaA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18010
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: 0.1 M sodium citrate, 20% PEG 3350, 0.1 M cacodylate, pH 7.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→137 Å / Num. all: 82558 / Num. obs: 82474 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 26.24 Å2 / Rsym value: 0.037 / Net I/σ(I): 25.2
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 11885 / Rsym value: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
BUSTER2.13.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gww

2gww


Resolution: 1.61→53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9548 / SU R Cruickshank DPI: 0.102 / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 4129 5.01 %RANDOM
Rwork0.1843 ---
all-82502 --
obs-82388 --
Displacement parametersBiso mean: 32.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.7234 Å20 Å20 Å2
2--1.6471 Å20 Å2
3---4.0763 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.61→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 10 804 5178
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018930HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0216258HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.972045SINUSOIDAL2
X-RAY DIFFRACTIONt_other_torsion13.81124HARMONIC2
LS refinement shellResolution: 1.61→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2496 324 5.52 %
Rwork0.1924 5549 -
all0.1956 5873 -
obs-5873 99.69 %
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)
10.1298-0.08620.31620.3774-0.05511.52920.0629-0.016-0.031-0.0627-0.00160.06410.0756-0.2039-0.0614-0.0147-0.0079-0.0178-0.04810.0067-0.07771.22274.033893.9219
20.17120.10610.30370.39230.10541.55030.0532-0.0043-0.02460.0398-0.0075-0.04560.06320.1656-0.0457-0.0177-0.001-0.0149-0.0569-0.0036-0.074625.38415.1245112.456
32.6270.1677-0.64320.94291.04163.59810.04250.05540.03050.1686-0.07620.13050.0912-0.10340.0337-0.0052-0.0413-0.0123-0.03760.0019-0.07348.92452.6817113.256
42.38880.37760.08751.5116-0.96884.44310.0306-0.0019-0.0027-0.0931-0.1087-0.10910.05430.0660.0781-0.01540.0328-0.0185-0.04630.0021-0.082517.91733.015193.4865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 800
2X-RAY DIFFRACTION2{ B|* }B1 - 800
3X-RAY DIFFRACTION3{ C|* }C488 - 510
4X-RAY DIFFRACTION4{ D|* }D488 - 511

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