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- PDB-2ykt: Crystal structure of the I-BAR domain of IRSp53 (BAIAP2) in compl... -

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Basic information

Entry
Database: PDB / ID: 2ykt
TitleCrystal structure of the I-BAR domain of IRSp53 (BAIAP2) in complex with an EHEC derived Tir peptide
Components
  • BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2
  • TRANSLOCATED INTIMIN RECEPTOR PROTEIN
KeywordsSIGNALING PROTEIN / NPY MOTIF / BINDING POCKET
Function / homology
Function and homology information


neuron projection branch point / dendritic spine cytoplasm / plasma membrane organization / actin crosslink formation / positive regulation of dendritic spine morphogenesis / cellular response to L-glutamate / protein localization to synapse / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton ...neuron projection branch point / dendritic spine cytoplasm / plasma membrane organization / actin crosslink formation / positive regulation of dendritic spine morphogenesis / cellular response to L-glutamate / protein localization to synapse / cadherin binding involved in cell-cell adhesion / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / presynaptic cytosol / neuron projection terminus / proline-rich region binding / postsynaptic cytosol / positive regulation of actin filament polymerization / dendrite development / positive regulation of excitatory postsynaptic potential / actin filament bundle assembly / CDC42 GTPase cycle / excitatory synapse / : / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic density, intracellular component / cellular response to epidermal growth factor stimulus / ruffle / RAC1 GTPase cycle / axonogenesis / secretory granule / dendritic shaft / synaptic membrane / filopodium / PDZ domain binding / transcription coregulator binding / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / adherens junction / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / insulin receptor signaling pathway / lamellipodium / regulation of cell shape / scaffold protein binding / microtubule / membrane => GO:0016020 / neuronal cell body / glutamatergic synapse / host cell plasma membrane / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain ...Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Translocated intimin receptor Tir / BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ESCHERICHIA COLI O157\:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
Authorsde Groot, J.C. / Schlueter, K. / Carius, Y. / Quedenau, C. / Vingadassalom, D. / Faix, J. / Weiss, S.M. / Reichelt, J. / Standfuss-Gabisch, C. / Lesser, C.F. ...de Groot, J.C. / Schlueter, K. / Carius, Y. / Quedenau, C. / Vingadassalom, D. / Faix, J. / Weiss, S.M. / Reichelt, J. / Standfuss-Gabisch, C. / Lesser, C.F. / Leong, J.M. / Heinz, D.W. / Buessow, K. / Stradal, T.E.B.
CitationJournal: Structure / Year: 2011
Title: Structural Basis for Complex Formation between Human Irsp53 and the Translocated Intimin Receptor Tir of Enterohemorrhagic E. Coli.
Authors: De Groot, J.C. / Schluter, K. / Carius, Y. / Quedenau, C. / Vingadassalom, D. / Faix, J. / Weiss, S.M. / Reichelt, J. / Standfuss-Gabisch, C. / Lesser, C.F. / Leong, J.M. / Heinz, D.W. / ...Authors: De Groot, J.C. / Schluter, K. / Carius, Y. / Quedenau, C. / Vingadassalom, D. / Faix, J. / Weiss, S.M. / Reichelt, J. / Standfuss-Gabisch, C. / Lesser, C.F. / Leong, J.M. / Heinz, D.W. / Bussow, K. / Stradal, T.E.B.
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2
B: TRANSLOCATED INTIMIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2373
Polymers30,1412
Non-polymers961
Water82946
1
A: BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2
B: TRANSLOCATED INTIMIN RECEPTOR PROTEIN
hetero molecules

A: BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2
B: TRANSLOCATED INTIMIN RECEPTOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4756
Polymers60,2834
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area8460 Å2
ΔGint-85.7 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.354, 187.362, 36.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BRAIN-SPECIFIC ANGIOGENESIS INHIBITOR 1-ASSOCIATED PROTEIN 2 / BAI-ASSOCIATED PROTEIN 2 / BAI1-ASSOCIATED PROTEIN 2 / PROTEIN BAP2 / FAS LIGAND-ASSOCIATED FACTOR ...BAI-ASSOCIATED PROTEIN 2 / BAI1-ASSOCIATED PROTEIN 2 / PROTEIN BAP2 / FAS LIGAND-ASSOCIATED FACTOR 3 / FLAF3 / INSULIN RECEPTOR SUBSTRATE P53/P58 / IRS-58 / IRSP53/58 / INSULIN RECEPTOR SUBSTRATE PROTEIN OF 53 KDA / IRSP53 / INSULIN RECEPTOR SUBSTRATE P53


Mass: 28849.842 Da / Num. of mol.: 1 / Fragment: I-BAR DOMAIN, RESIDUES 1-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: Q9UQB8
#2: Protein/peptide TRANSLOCATED INTIMIN RECEPTOR PROTEIN / TRANSLOCATED INTIMIN RECEPTOR


Mass: 1291.410 Da / Num. of mol.: 1 / Fragment: RESIDUES 452-463 / Source method: obtained synthetically / Details: C-TERMINAL AMIDE / Source: (synth.) ESCHERICHIA COLI O157\:H7 (bacteria) / References: UniProt: C6UYL8
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.73 Å3/Da / Density % sol: 54.63 % / Description: NONE
Crystal growDetails: 16% (W/V) PEG 3350, 0.3M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2009 / Details: MIRRORS
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.11→9.44 Å / Num. obs: 18190 / % possible obs: 99.8 % / Observed criterion σ(I): 3.1 / Redundancy: 12.7 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.13
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.13 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y2O

1y2o


Resolution: 2.11→9.44 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.071 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27604 895 5 %RANDOM
Rwork0.23336 ---
obs0.23559 17006 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---3.19 Å20 Å2
3---2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.11→9.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 5 46 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.972657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10525.248101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.39715393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1691512
X-RAY DIFFRACTIONr_chiral_restr0.1330.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.51198
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13121911
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5063780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7574.5739
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 64 -
Rwork0.3 1208 -
obs--100 %
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)
10.15450.08440.06391.43540.78180.57920.00890.004-0.0059-0.001-0.02150.0138-0.0143-0.03320.01250.0468-0.0009-0.00210.07620.03850.0484-14.2686-20.82228.3271
21.92211.331-0.31092.09940.11874.5517-0.032-0.141-0.4760.08450.05710.08860.26640.1707-0.02510.2688-0.03360.01070.25810.01690.3048-15.2655-33.4759.6503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 234
2X-RAY DIFFRACTION2B452 - 463

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