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- PDB-4iio: Crystal Structure of the Second SH3 Domain of ITSN2 Bound with a ... -

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Basic information

Entry
Database: PDB / ID: 4iio
TitleCrystal Structure of the Second SH3 Domain of ITSN2 Bound with a Synthetic Peptide
Components
  • Intersectin-2
  • Synthetic Peptide
KeywordsENDOCYTOSIS / Structural Genomics / Structural Genomics Consortium / SGC / SH3 domain / ITSN2 / synthetic peptide / Protein-peptide complex
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / positive regulation of dendrite extension / endosomal transport / positive regulation of Rho protein signal transduction / intracellular vesicle / RHOU GTPase cycle / guanyl-nucleotide exchange factor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane ...clathrin-dependent synaptic vesicle endocytosis / positive regulation of dendrite extension / endosomal transport / positive regulation of Rho protein signal transduction / intracellular vesicle / RHOU GTPase cycle / guanyl-nucleotide exchange factor activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic membrane / molecular adaptor activity / cell differentiation / centrosome / calcium ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Intersectin-2, first SH3 domain / Intersectin-2, second SH3 domain / Intersectin-2, third SH3 domain / Intersectin-2, fourth SH3 domain / Intersectin-2, fifth SH3 domain / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain ...Intersectin-2, first SH3 domain / Intersectin-2, second SH3 domain / Intersectin-2, third SH3 domain / Intersectin-2, fourth SH3 domain / Intersectin-2, fifth SH3 domain / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / SH3 Domains / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, A. / Guan, X. / Huang, H. / Gu, J. / Tempel, W. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Second SH3 Domain of ITSN2 Bound with a Synthetic Peptide
Authors: Guan, X. / Dong, A. / Huang, H. / Gu, J. / Tempel, W. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 10, 2021Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn ...pdbx_distant_solvent_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intersectin-2
B: Intersectin-2
C: Synthetic Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,26120
Polymers16,1293
Non-polymers13217
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-32 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.053, 48.053, 112.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Intersectin-2 / SH3 domain-containing protein 1B / SH3P18 / SH3P18-like WASP-associated protein


Mass: 7362.409 Da / Num. of mol.: 2 / Fragment: UNP residues 901-955
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN2, KIAA1256, SH3D1B, SWAP / Plasmid: pHH0239 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZM3
#2: Protein/peptide Synthetic Peptide


Mass: 1404.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized

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Non-polymers , 4 types, 176 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1 M (NH4)2SO4, and 0.1 M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 13, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 16192 / Num. obs: 16192 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.312 / Net I/σ(I): 28.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.737.80.4758030.214199.6
1.73-1.76100.4147890.231100
1.76-1.7911.20.3648140.2511100
1.79-1.8311.70.3228020.2691100
1.83-1.8711.80.2418060.2691100
1.87-1.9111.80.2198100.3041100
1.91-1.9611.90.1677920.2971100
1.96-2.0211.90.1388280.2891100
2.02-2.07120.1268080.331100
2.07-2.14120.1057940.2891100
2.14-2.2212.10.0928050.2721100
2.22-2.3112.10.0878290.341100
2.31-2.4112.20.0727990.2771100
2.41-2.5412.20.0678130.2721100
2.54-2.712.30.0568100.2851100
2.7-2.9112.30.0458030.2861100
2.91-3.212.40.0348270.3071100
3.2-3.6612.40.0298040.4141100
3.66-4.6112.40.0278160.5061100
4.61-5011.60.0278400.466199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
PHASER2.1.4phasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J3T

1j3t


Resolution: 1.7→27.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2072 / WRfactor Rwork: 0.1801 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8635 / SU B: 2.112 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1211 / SU Rfree: 0.1144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 810 5 %RANDOM
Rwork0.1935 ---
obs0.1951 15313 99.81 %-
all-15313 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.57 Å2 / Biso mean: 21.0377 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 21 159 1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191203
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.911661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.54324.56157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.567153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021941
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 59 -
Rwork0.303 1109 -
all-1168 -
obs--99.15 %

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