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- PDB-3gf9: Crystal structure of human Intersectin 2 RhoGEF domain -

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Basic information

Entry
Database: PDB / ID: 3gf9
TitleCrystal structure of human Intersectin 2 RhoGEF domain
ComponentsIntersectin 2
KeywordsENDOCYTOSIS / Structural genomics consortium / guanine nucleotide exchange factor / SGC / SH3 DOMAIN
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 / endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis ...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 / endocytosis / 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 / Dbl Homology Domain; Chain A / Dbl homology (DH) 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. / 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. / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Intersectin 2 / Intersectin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsShen, Y. / Tong, Y. / Tempel, W. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Intersectin 2 RhoGEF domain
Authors: Shen, Y. / Tong, Y. / Tempel, W. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 15, 2017Group: Data collection / Refinement description / Category: phasing / refine / Item: _refine.pdbx_starting_model
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Intersectin 2


Theoretical massNumber of molelcules
Total (without water)34,0206
Polymers34,0201
Non-polymers05
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.249, 29.616, 86.150
Angle α, β, γ (deg.)90.000, 121.060, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Intersectin 2


Mass: 34019.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN2 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-V2R pRARE2 / References: UniProt: A6H8W8, UniProt: Q9NZM3*PLUS
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 1:100 papain protease was added, SDS-PAGE indicated that the crystallized protein had a molecular weight of 23kDa, pH 5.5, VAPOR ...Details: 25% PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 1:100 papain protease was added, SDS-PAGE indicated that the crystallized protein had a molecular weight of 23kDa, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8098 / % possible obs: 97.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Χ2: 1.581 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.592.40.6217072.40387.7
2.59-2.692.50.5097822.03193.1
2.69-2.822.80.3747631.84395.9
2.82-2.9630.2688251.47198.4
2.96-3.153.30.1918001.47799.1
3.15-3.393.40.1258321.39999.8
3.39-3.733.40.0798391.42999.5
3.73-4.273.40.0598201.42699.4
4.27-5.383.20.0488421.44599.5
5.38-503.20.0358881.52999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KI1

1ki1


Resolution: 2.5→36.899 Å / FOM work R set: 0.787 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 376 4.68 %
Rwork0.221 --
obs0.224 8032 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.037 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 138.46 Å2 / Biso mean: 57.13 Å2 / Biso min: 31.85 Å2
Baniso -1Baniso -2Baniso -3
1--12.36 Å2-0 Å2-0.64 Å2
2---14.453 Å20 Å2
3----15.529 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 5 0 1414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081429
X-RAY DIFFRACTIONf_angle_d1.1371927
X-RAY DIFFRACTIONf_chiral_restr0.069226
X-RAY DIFFRACTIONf_plane_restr0.004246
X-RAY DIFFRACTIONf_dihedral_angle_d16.748528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.590.3371020.3012395249792
2.862-3.6050.2941260.2312599272599
3.605-36.9030.2451480.1862662281099
Refinement TLS params.Method: refined / Origin x: -17.8023 Å / Origin y: -14.7974 Å / Origin z: 6.6302 Å
111213212223313233
T0.4104 Å20.0148 Å2-0.0519 Å2-0.4491 Å2-0.0545 Å2--0.483 Å2
L1.5088 °20.001 °2-0.5923 °2-3.2765 °2-0.9155 °2--1.7621 °2
S-0.0699 Å °-0.1901 Å °0.0173 Å °0.4552 Å °0.0412 Å °-0.3561 Å °-0.2216 Å °0.3365 Å °-0 Å °
Refinement TLS groupSelection: chain A / Selection details: chain A

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