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- PDB-2gdc: Structure of Vinculin VD1 / IpaA560-633 complex -

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Basic information

Entry
Database: PDB / ID: 2gdc
TitleStructure of Vinculin VD1 / IpaA560-633 complex
Components
  • Invasin ipaA
  • Vinculin
KeywordsCELL INVASION / IpaA-Vinculin complex / Shigella flexneri / Helical bundle conversion
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / 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 / terminal web / epithelial cell-cell adhesion ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / 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 / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / 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 / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / actin cytoskeleton / actin binding / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / protein homodimerization activity / protein-containing complex / extracellular region / plasma membrane / 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
Vinculin / Invasin IpaA
Similarity search - Component
Biological speciesGallus gallus (chicken)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsHamiaux, C. / van Eerde, A. / Parsot, C. / Broos, J. / Dijkstra, B.W.
CitationJournal: Embo Rep. / Year: 2006
Title: Structural mimicry for vinculin activation by IpaA, a virulence factor of Shigella flexneri.
Authors: Hamiaux, C. / van Eerde, A. / Parsot, C. / Broos, J. / Dijkstra, B.W.
History
DepositionMar 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Remark 999SEQUENCE The crystallized sequence of Invasin ipaA (chain B in the coordinates) is ...SEQUENCE The crystallized sequence of Invasin ipaA (chain B in the coordinates) is IDKNHAIYEKAKEVSSALSKVLSKIDDTSAELLTDDISDLKN NNDITAENNNIYKAAKDVTTSLSKVLKNINKD (residues 560-633 of the SWS entry IPAA_SHIFL). The fragment in the coordinates corresponds either to residues 564-584 or 610-630. An average helix was modelled in which the 11 identical residues were build with their side chains. The 10 non-identical residues, which showed no density for their side chains, were build as unknown residues (UNK).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: Invasin ipaA


Theoretical massNumber of molelcules
Total (without water)31,8882
Polymers31,8882
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-25 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.684, 68.326, 96.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vinculin / / Metavinculin


Mass: 29788.379 Da / Num. of mol.: 1 / Fragment: VD1 domain (RESIDUES 0-265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Plasmid: pMAL-p2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P12003
#2: Protein/peptide Invasin ipaA / 70 kDa antigen


Mass: 2099.645 Da / Num. of mol.: 1 / Fragment: C-terminal fragment (RESIDUES 560-633)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaA / Plasmid: pGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P18010
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 10% 2-propanol, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.74→15.19 Å / Num. obs: 9559 / % possible obs: 99 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.74-2.891004.80.352.113660.351
2.89-3.061004.80.24713110.24
3.06-3.2799.94.80.17312250.174
3.27-3.5499.84.80.12311420.127
3.54-3.8799.84.80.08410580.088
3.87-4.3399.54.70.0509720.057
4.33-599.44.70.0438480.047
5-6.13994.70.0527360.053
6.13-8.6698.84.50.0435870.04
8.66-41.74784.20.0372620.038

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SYQ

1syq


Resolution: 2.74→15.18 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.882 / SU B: 16.459 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 0.98 / ESU R Free: 0.387 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 467 4.919 %RANDOM
Rwork0.247 ---
all0.25 9974 --
obs0.24966 9493 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.077 Å20 Å20 Å2
2--7.092 Å20 Å2
3----6.015 Å2
Refinement stepCycle: LAST / Resolution: 2.74→15.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 14 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9832724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70125.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84115386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4591512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.2955
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21421
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6851.51345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17922104
X-RAY DIFFRACTIONr_scbond_it1.6933749
X-RAY DIFFRACTIONr_scangle_it2.9134.5620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.74-2.8090.444290.3236400.329669100
2.809-2.8830.234380.3096260.305664100
2.883-2.9640.308350.265950.26363199.842
2.964-3.0510.361250.2975900.299615100
3.051-3.1470.32340.3065830.30761899.838
3.147-3.2520.485280.295600.298588100
3.252-3.3690.326230.2715410.27356699.647
3.369-3.50.357310.2465210.25155399.819
3.5-3.6460.287250.2384960.24152399.618
3.646-3.8130.304300.2574920.25952599.429
3.813-4.0060.244300.2344470.23448099.375
4.006-4.230.225230.2134350.21446299.134
4.23-4.4980.31590.1924350.19444998.886
4.498-4.8230.25290.1973880.242298.815
4.823-5.230.209180.2273680.22638899.485
5.23-5.7630.351160.2613390.26436198.338
5.763-6.50.62670.293080.29632098.438
6.5-7.620.236110.2472740.24629397.27
7.62-9.6310.228170.1892240.19224598.367
9.631-15.1810.32590.2581640.26118593.514

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