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- PDB-1y2o: Structure of N-terminal domain IRSp53/BAIAP2 -

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Basic information

Entry
Database: PDB / ID: 1y2o
TitleStructure of N-terminal domain IRSp53/BAIAP2
ComponentsBAI1-associated protein 2 isoform 1
KeywordsSIGNALING PROTEIN / cell motility / filopodia / actin bundling
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 / MAD / Resolution: 2.2 Å
AuthorsMillard, T.H. / Bompard, G. / Heung, M.-Y. / Dafforn, T.R. / Scott, D.J. / Machesky, L.M. / Futterer, K.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis of filopodia formation induced by the IRSp53/MIM homology domain of human IRSp53
Authors: Millard, T.H. / Bompard, G. / Heung, M.-Y. / Dafforn, T.R. / Scott, D.J. / Machesky, L.M. / Futterer, K.
History
DepositionNov 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAI1-associated protein 2 isoform 1
B: BAI1-associated protein 2 isoform 1


Theoretical massNumber of molelcules
Total (without water)57,9602
Polymers57,9602
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-77 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.879, 64.164, 74.586
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BAI1-associated protein 2 isoform 1 / BAIAP2


Mass: 28979.770 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9UQB8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.92 Å3/Da / Density % sol: 33.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9781, 0.9776, 0.9649
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97811
20.97761
30.96491
ReflectionResolution: 2.2→47.8 Å / Num. all: 22459 / Num. obs: 22459 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 25.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 8.4 / Num. unique all: 3133 / Rsym value: 0.192 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→47.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.899 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.493 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26683 1127 5 %RANDOM
Rwork0.22831 ---
all0.23021 21208 --
obs0.23021 21208 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.328 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å2-1.54 Å2
2---0.07 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 0 221 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223998
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9735353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2065494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11325.389193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8215799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022964
X-RAY DIFFRACTIONr_nbd_refined0.1960.21985
X-RAY DIFFRACTIONr_nbtor_refined0.2890.22768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.225
X-RAY DIFFRACTIONr_mcbond_it0.7231.52564
X-RAY DIFFRACTIONr_mcangle_it1.0623920
X-RAY DIFFRACTIONr_scbond_it1.82931635
X-RAY DIFFRACTIONr_scangle_it2.8224.51433
LS refinement shellResolution: 2.2→2.319 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.33 157 -
Rwork0.249 2858 -
obs--94.13 %
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)
10.3333-0.18040.54870.4508-1.06216.11220.01730.057-0.0029-0.0583-0.0949-0.06120.12220.35350.0776-0.2405-0.00720.0289-0.09830.0191-0.0573-1.92428.04928.928
20.3652-0.14520.99220.463-1.27317.3461-0.0557-0.09940.0170.01330.0363-0.00040.0845-0.30660.0193-0.2201-0.00360.0251-0.09430.0033-0.0756-5.27721.11170.333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2471 - 247
2X-RAY DIFFRACTION2BB1 - 2471 - 247

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