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- PDB-3rnj: Crystal structure of the SH3 domain from IRSp53 (BAIAP2) -

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Basic information

Entry
Database: PDB / ID: 3rnj
TitleCrystal structure of the SH3 domain from IRSp53 (BAIAP2)
ComponentsBrain-specific angiogenesis inhibitor 1-associated protein 2
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / Beta barrel / Protein interaction domain / Proline-rich motifs
Function / homology
Function and homology information


neuron projection branch point / dendritic spine cytoplasm / actin crosslink formation / plasma membrane organization / cadherin binding involved in cell-cell adhesion / positive regulation of dendritic spine morphogenesis / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / protein localization to synapse / cellular response to L-glutamate ...neuron projection branch point / dendritic spine cytoplasm / actin crosslink formation / plasma membrane organization / cadherin binding involved in cell-cell adhesion / positive regulation of dendritic spine morphogenesis / cytoskeletal anchor activity / regulation of modification of postsynaptic actin cytoskeleton / protein localization to synapse / cellular response to L-glutamate / neuron projection terminus / proline-rich region binding / positive regulation of actin filament polymerization / dendrite development / actin filament bundle assembly / CDC42 GTPase cycle / postsynaptic cytosol / excitatory synapse / positive regulation of excitatory postsynaptic potential / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic density, intracellular component / presynaptic cytosol / ruffle / RAC1 GTPase cycle / cellular response to epidermal growth factor stimulus / axonogenesis / dendritic shaft / secretory granule / transcription coregulator binding / PDZ domain binding / filopodium / adherens junction / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / synaptic membrane / 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 / neuronal cell body / glutamatergic synapse / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains ...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. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-EDT / ISOPROPYL ALCOHOL / BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSimister, P.C. / Barilari, M. / Muniz, J.R.C. / Dente, L. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Vollmar, M. / Chaikuad, A. / Raynor, J. ...Simister, P.C. / Barilari, M. / Muniz, J.R.C. / Dente, L. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Vollmar, M. / Chaikuad, A. / Raynor, J. / Tregubova, A. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Feller, S.M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the SH3 domain from IRSp53 (BAIAP2)
Authors: Simister, P.C. / Barilari, M. / Muniz, J.R.C. / Dente, L. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Vollmar, M. / Chaikuad, A. / Raynor, J. / Tregubova, A. / Arrowsmith, C.H. / M ...Authors: Simister, P.C. / Barilari, M. / Muniz, J.R.C. / Dente, L. / Knapp, S. / von Delft, F. / Filippakopoulos, P. / Vollmar, M. / Chaikuad, A. / Raynor, J. / Tregubova, A. / Arrowsmith, C.H. / M Edwards, A. / Weigelt, J. / Bountra, C. / Feller, S.M. / Structural Genomics Consortium (SGC)
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brain-specific angiogenesis inhibitor 1-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0516
Polymers7,5131
Non-polymers5395
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.960, 36.640, 58.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 7512.523 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 375-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAIAP2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UQB8
#2: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium acetate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→31 Å / Num. all: 10736 / Num. obs: 10716 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 17.6 Å2 / Net I/σ(I): 9.7
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.43 / Num. unique all: 408 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG5, 1Y6E, 1GNE, 1DUG and 3QMZ

1bg5

1y6e

1gne

1dug

3qmz


Resolution: 1.5→23.2 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 536 5.01 %Random
Rwork0.197 ---
all0.198 10716 --
obs0.198 10700 99.7 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.011 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1656 Å2-0 Å20 Å2
2---7.8872 Å2-0 Å2
3---12.0528 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 36 86 652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004604
X-RAY DIFFRACTIONf_angle_d0.944813
X-RAY DIFFRACTIONf_dihedral_angle_d18.548243
X-RAY DIFFRACTIONf_chiral_restr0.05480
X-RAY DIFFRACTIONf_plane_restr0.004106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.6510.38541310.33112472X-RAY DIFFRACTION100
1.651-1.88980.24241320.22462506X-RAY DIFFRACTION100
1.8898-2.38050.21411330.18132528X-RAY DIFFRACTION100
2.3805-23.19620.17451400.16522658X-RAY DIFFRACTION100
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)
10.05450.0774-0.05460.1106-0.07780.0550.05810.02930.0149-0.0601-0.0528-0.02960.0054-0.0044-0.01040.1268-0.06760.0020.14450.0583-0.004222.0209-4.596817.0634
20.1794-0.05990.04090.336-0.00050.1893-0.0538-0.0056-0.00920.00780.02010.0382-0.0109-0.03850.00930.0785-0.0087-0.00520.071-0.00410.070110.6821.9543-1.3668
30.06420.0307-0.0140.02790.00850.06050.0359-0.036-0.00540.0385-0.0120.00040.0107-0.0372-0.00720.0169-0.0163-0.00520.0206-0.00370.042312.5152-1.17874.2267
40.33410.03470.06680.40160.0180.2573-0.0129-0.0399-0.0210.02350.0044-0.03420.0221-0.06510.00430.0270.00870.0040.00590.00140.036413.28342.9083.596
50.1897-0.00080.01590.3775-0.00650.1264-0.0182-0.0162-0.0348-0.01270.032-0.0879-0.0001-0.0247-0.0030.02360.0068-0.00330.01680.01050.06169.3937-1.00223.7239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 370:376)
2X-RAY DIFFRACTION2chain 'A' and (resseq 377:396)
3X-RAY DIFFRACTION3chain 'A' and (resseq 397:409)
4X-RAY DIFFRACTION4chain 'A' and (resseq 410:422)
5X-RAY DIFFRACTION5chain 'A' and (resseq 423:436)

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