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- PDB-4iim: Crystal structure of the Second SH3 Domain of ITSN1 bound with a ... -

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Basic information

Entry
Database: PDB / ID: 4iim
TitleCrystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide
Components
  • Intersectin-1
  • peptide ligand
KeywordsENDOCYTOSIS / SH3 Domain / ITSN1 / Structural Genomics Consortium / SGC / protein-peptide complex
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / protein localization / recycling endosome / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / lamellipodium / Clathrin-mediated endocytosis / nuclear envelope / molecular adaptor activity / neuron projection / intracellular signal transduction / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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 / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / SH3 type barrels. / 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: 1.8 Å
AuthorsDong, A. / Guan, X. / Huang, H. / Wernimont, A. / Gu, J. / 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 ITSN1 bound with a synthetic peptide
Authors: Guan, X. / Dong, A. / Huang, H. / Wernimont, A. / Gu, J. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 / 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: Intersectin-1
C: peptide ligand
B: Intersectin-1
D: peptide ligand
E: peptide ligand


Theoretical massNumber of molelcules
Total (without water)20,09316
Polymers20,0935
Non-polymers011
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Intersectin-1
C: peptide ligand

B: Intersectin-1
D: peptide ligand
E: peptide ligand


Theoretical massNumber of molelcules
Total (without water)20,09316
Polymers20,0935
Non-polymers011
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation3_544-x,y-1/2,-z-1/21
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-30 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.048, 51.393, 69.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Intersectin-1 / SH3 domain-containing protein 1A / SH3P17


Mass: 7883.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN1, ITSN, SH3D1A / Plasmid: pHH0239 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15811
#2: Protein/peptide peptide ligand


Mass: 1441.591 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic sequence
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M NaCitrate and 0.1 M Tris, pH 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: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 13540 / Num. obs: 13540 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.03 / Χ2: 0.186 / Net I/σ(I): 28.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.836.80.3456510.125193.7
1.83-1.867.30.3136120.117190.5
1.86-1.97.40.2656580.129195.4
1.9-1.947.70.1836500.146193.4
1.94-1.987.70.1676480.141193.6
1.98-2.037.80.1376480.143194.5
2.03-2.087.80.1176530.167194.6
2.08-2.1380.0986620.152194.4
2.13-2.27.80.0916560.168196
2.2-2.277.90.0776710.203194.4
2.27-2.357.90.0716870.183197.2
2.35-2.447.90.0646680.175195.3
2.44-2.557.90.0526710.17196.1
2.55-2.697.80.0436960.176198.2
2.69-2.867.70.0326860.184197.3
2.86-3.087.80.0286900.191197.6
3.08-3.397.70.0216950.22197.9
3.39-3.887.70.0177170.256198.2
3.88-4.887.50.0147230.281198.9
4.88-506.50.0167980.362198.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREP11phasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J3T
Resolution: 1.8→29.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8283 / SU B: 3.253 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1465 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 664 4.9 %RANDOM
Rwork0.1875 ---
all0.19016 ---
obs0.1902 13452 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.26 Å2 / Biso mean: 26.3598 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2--1.36 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 11 99 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021268
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.8981733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1724.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18715208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.982153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021999
X-RAY DIFFRACTIONr_mcbond_it1.8132.444573
X-RAY DIFFRACTIONr_mcangle_it2.9163.639711
X-RAY DIFFRACTIONr_scbond_it2.1732.586695
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 53 -
Rwork0.296 879 -
all-932 -
obs--92.46 %

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