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- PDB-2ibf: Human vinculin's head domain (Vh1, residues 1-258) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2ibf
TitleHuman vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587)
Components
  • Invasin ipaA
  • Vinculin
KeywordsCELL ADHESION / STRUCTURAL PROTEIN
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
Invasin IpaA / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsIzard, T.
CitationJournal: Embo J. / Year: 2007
Title: Vinculin binding in its closed conformation by a helix addition mechanism.
Authors: Nhieu, G.T. / Izard, T.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Invasin ipaA
D: Invasin ipaA


Theoretical massNumber of molelcules
Total (without water)35,5313
Polymers35,5313
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.478, 154.478, 154.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Vinculin / / Metavinculin


Mass: 30026.590 Da / Num. of mol.: 1 / Fragment: Head domain (Vh1): Residues 1-258
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: 2752.103 Da / Num. of mol.: 2 / Fragment: Vinculin binding sites: Residues 565-587
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.41 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→109.11 Å / Num. obs: 10911 / Biso Wilson estimate: 95.717 Å2
Reflection shellHighest resolution: 3.2 Å

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Processing

SoftwareName: BUSTER-TNT / Version: 1.3.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→109.11 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1070 9.88 %RANDOM
Rwork0.2426 ---
obs0.2452 10834 98.99 %-
Displacement parametersBiso mean: 74.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.73 Å
Refinement stepCycle: LAST / Resolution: 3.2→109.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 0 0 2359
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00523872
X-RAY DIFFRACTIONt_angle_deg0.90332152
X-RAY DIFFRACTIONt_dihedral_angle_d30.0485400
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.003692
X-RAY DIFFRACTIONt_gen_planes0.0093295
X-RAY DIFFRACTIONt_it2.942238420
X-RAY DIFFRACTIONt_nbd0.273995
LS refinement shellResolution: 3.2→3.39 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2981 186 11.03 %
Rwork0.2519 1500 -
all25.71 1686 -
obs--98.99 %

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