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- PDB-1wdz: Crystal structure of RCB domain of IRSp53 -

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Basic information

Entry
Database: PDB / ID: 1wdz
TitleCrystal structure of RCB domain of IRSp53
Componentsinsulin receptor substrate p53
KeywordsSIGNALING PROTEIN / cellular signaling protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / dendritic shaft / secretory granule / 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 / 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. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...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
BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.63 Å
AuthorsMurayama, K. / Suetsugu, S. / Seto, A. / Shirouzu, M. / Takenawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of RCB domain of IRSp53
Authors: Murayama, K. / Suetsugu, S. / Seto, A. / Shirouzu, M. / Takenawa, T. / Yokoyama, S.
History
DepositionMay 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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: insulin receptor substrate p53
B: insulin receptor substrate p53


Theoretical massNumber of molelcules
Total (without water)55,1952
Polymers55,1952
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-58 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.833, 69.258, 68.715
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein insulin receptor substrate p53 / IRSp53


Mass: 27597.312 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQB8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 27% PEG4000, 0.09M Tris pH8.5, 0.19M Sodium acetate, 3.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 22, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 15858 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 26.1
Reflection shellResolution: 2.63→2.75 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.303 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.63→41.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 576339.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1593 10.1 %RANDOM
Rwork0.235 ---
obs0.235 15846 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.4682 Å2 / ksol: 0.293805 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--12.78 Å20 Å212.93 Å2
2--1.24 Å20 Å2
3---11.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.63→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 0 70 3712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.63→2.79 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 276 10.7 %
Rwork0.32 2314 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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