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- PDB-2hsq: Human vinculin (head domain, Vh1, residues 1-258) in complex with... -

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Basic information

Entry
Database: PDB / ID: 2hsq
TitleHuman vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site 2 (residues 565-587)
Components
  • Invasin ipaA
  • Vinculin
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / protein complex
Function / homology
Function and homology information


positive regulation of actin filament depolymerization / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding ...positive regulation of actin filament depolymerization / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / vinculin binding / apical junction assembly / costamere / 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 / Smooth Muscle Contraction / negative regulation of cell migration / cell projection / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / 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 / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / cell-cell junction / Platelet degranulation / extracellular vesicle / actin binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / 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
Invasin IpaA / Vinculin / IpaA
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.97 Å
AuthorsIzard, T.
CitationJournal: J.Cell Biol. / Year: 2006
Title: Shigella applies molecular mimicry to subvert vinculin and invade host cells.
Authors: Izard, T. / Tran Van Nhieu, G. / Bois, P.R.
History
DepositionJul 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)32,5262
Polymers32,5262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-26 kcal/mol
Surface area15810 Å2
MethodPISA
2
A: Vinculin
B: Invasin ipaA
x 24


Theoretical massNumber of molelcules
Total (without water)780,63548
Polymers780,63548
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area115390 Å2
ΔGint-877 kcal/mol
Surface area317460 Å2
MethodPISA
3
A: Vinculin
B: Invasin ipaA
x 6


Theoretical massNumber of molelcules
Total (without water)195,15912
Polymers195,15912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation37_546y+1/2,x-1/2,-z+3/21
crystal symmetry operation42_645-x+3/2,z-1/2,y+1/21
crystal symmetry operation48_656-z+3/2,-y+1/2,-x+3/21
Buried area28880 Å2
ΔGint-205 kcal/mol
Surface area79330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.170, 203.170, 203.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Vinculin / Metavinculin


Mass: 30026.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#2: Protein/peptide Invasin ipaA / 70 kDa antigen


Mass: 2499.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaA / Production host: Escherichia coli (E. coli) / References: UniProt: P18010, UniProt: Q6XVZ2*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.1 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 22-ID1
SYNCHROTRONAPS 19-ID2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.97→58.72 Å / Num. obs: 6410 / Biso Wilson estimate: 130.396 Å2

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Processing

SoftwareName: BUSTER-TNT / Version: 1.3.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.97→58 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3162 636 9.95 %RANDOM
Rwork0.286 ---
obs0.289 6392 98.41 %-
all-7028 --
Displacement parametersBiso mean: 157.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.348 Å
Refinement stepCycle: LAST / Resolution: 3.97→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 0 0 2239
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00222712
X-RAY DIFFRACTIONt_angle_deg0.44530612
X-RAY DIFFRACTIONt_dihedral_angle_d32.8495080
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.002632
X-RAY DIFFRACTIONt_gen_planes0.0053155
X-RAY DIFFRACTIONt_it2.431226720
X-RAY DIFFRACTIONt_nbd0.0271285
LS refinement shellResolution: 3.97→4.21 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3124 99 9.9 %
Rwork0.2977 901 -
all29.92 1000 -
obs--98.41 %

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