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

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Basic information

Entry
Database: PDB / ID: 2gww
TitleHuman vinculin (head domain, Vh1, residues 1-258) in complex with Shigella's IpaA vinculin binding site (residues 602-633)
Components
  • 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 / 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 / Signaling by RAF1 mutants / extracellular vesicle / 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
: / Invasin IpaA / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.72 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
DepositionMay 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 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

Downloads & links

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Assembly

Deposited unit
A: vinculin
B: IpaA


Theoretical massNumber of molelcules
Total (without water)33,3372
Polymers33,3372
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-23 kcal/mol
Surface area15080 Å2
MethodPISA
2
A: vinculin
B: IpaA
x 6


Theoretical massNumber of molelcules
Total (without water)200,02412
Polymers200,02412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation42_454-x-1/4,z+1/4,y-1/41
crystal symmetry operation46_455z-1/4,-y+3/4,x+1/41
Buried area29520 Å2
ΔGint-214 kcal/mol
Surface area73800 Å2
MethodPISA
3
A: vinculin
B: IpaA

A: vinculin
B: IpaA

A: vinculin
B: IpaA


Theoretical massNumber of molelcules
Total (without water)100,0126
Polymers100,0126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area11430 Å2
ΔGint-100 kcal/mol
Surface area40230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.310, 151.310, 151.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein vinculin /


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


Mass: 3310.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 32307018, UniProt: P18010*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.33 %

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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: 2.72→99 Å / Num. obs: 7633 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 73.693 Å2

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Processing

SoftwareName: BUSTER-TNT / Version: 1.3.2 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.72→99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: SOME OF THE WATER MOLECULES ARE PLACED IN DISORDERED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 362 4.75 %RANDOM
Rwork0.2292 ---
all0.2323 7619 --
obs0.2323 7619 92.14 %-
Displacement parametersBiso mean: 79.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.4285 Å
Refinement stepCycle: LAST / Resolution: 2.72→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 82 2282
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00422282
X-RAY DIFFRACTIONt_angle_deg0.56630062
X-RAY DIFFRACTIONt_dihedral_angle_d22.7144980
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.003652
X-RAY DIFFRACTIONt_gen_planes0.0053085
X-RAY DIFFRACTIONt_it15.408222420
X-RAY DIFFRACTIONt_nbd0.088875
LS refinement shellResolution: 2.72→2.88 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3438 44 5.46 %
Rwork0.2937 762 -
all29.69 806 -
obs--92.14 %

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