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- PDB-3jv3: Structure of SH3E-DH unit of murine intersectin-1L -

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Basic information

Entry
Database: PDB / ID: 3jv3
TitleStructure of SH3E-DH unit of murine intersectin-1L
ComponentsIntersectin-1
KeywordsPROTEIN BINDING / SH3 domain / DH domain / guanine nucleotide exchange factor / autoinhibition / domain-swapped / Cell junction / Cell projection / Endocytosis / Membrane / Phosphoprotein / Synapse / Synaptosome
Function / homology
Function and homology information


presynaptic endocytic zone / RHOQ GTPase cycle / positive regulation of caveolin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / EPHB-mediated forward signaling / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / positive regulation of growth hormone secretion ...presynaptic endocytic zone / RHOQ GTPase cycle / positive regulation of caveolin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / EPHB-mediated forward signaling / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / positive regulation of growth hormone secretion / Cargo recognition for clathrin-mediated endocytosis / postsynaptic actin cytoskeleton / Clathrin-mediated endocytosis / regulation of modification of postsynaptic actin cytoskeleton / apical dendrite / kinase activator activity / regulation of postsynapse organization / endosomal transport / small GTPase-mediated signal transduction / positive regulation of Rho protein signal transduction / intracellular vesicle / positive regulation of dendritic spine development / exocytosis / calyx of Held / synaptic vesicle endocytosis / endocytic vesicle / clathrin-coated pit / guanyl-nucleotide exchange factor activity / recycling endosome / protein transport / lamellipodium / presynaptic membrane / nuclear envelope / neuron apoptotic process / negative regulation of neuron apoptotic process / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / molecular adaptor activity / neuronal cell body / glutamatergic synapse / 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 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...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 / Dbl Homology Domain; Chain A / Dbl homology (DH) 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 / 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 / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsAhmad, K.F.
CitationJournal: Plos One / Year: 2010
Title: The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin.
Authors: Ahmad, K.F. / Lim, W.A.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: Intersectin-1
B: Intersectin-1


Theoretical massNumber of molelcules
Total (without water)65,4432
Polymers65,4432
Non-polymers00
Water1,24369
1
A: Intersectin-1


Theoretical massNumber of molelcules
Total (without water)32,7221
Polymers32,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intersectin-1


Theoretical massNumber of molelcules
Total (without water)32,7221
Polymers32,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.044, 67.044, 341.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Intersectin-1 / EH and SH3 domains protein 1


Mass: 32721.740 Da / Num. of mol.: 2 / Fragment: SH3 5 and DH domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itsn1, Ese1, Itsn / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z0R4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.7 M LiSO4, 0.1M Hepes pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2006
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionRedundancy: 7.6 % / Av σ(I) over netI: 38.76 / Number: 274736 / Rmerge(I) obs: 0.05 / Χ2: 0.91 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 36102 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175098.410.0241.1127.2
4.15.1799.810.0481.0837.5
3.584.110010.0541.0897.8
3.263.5899.910.051.0297.9
3.023.2610010.0790.9047.9
2.853.0210010.1310.8528
2.72.8510010.1890.8148
2.592.799.910.2940.7338
2.492.5999.910.3690.7217.5
2.42.4997.110.3860.7116.3
ReflectionResolution: 2.4→50 Å / Num. all: 36283 / Num. obs: 36102 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.05 / Χ2: 0.91 / Net I/σ(I): 38.764
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.496.30.38634230.71197.1
2.49-2.597.50.36935560.72199.9
2.59-2.780.29435430.73399.9
2.7-2.8580.18935470.814100
2.85-3.0280.13135890.852100
3.02-3.267.90.07935850.904100
3.26-3.587.90.0536131.02999.9
3.58-4.17.80.05436541.089100
4.1-5.177.50.04837111.08399.8
5.17-507.20.02438811.11298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.26 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1701 4.7 %Random
Rwork0.248 ---
obs0.25 34314 94.7 %-
all-36243 --
Solvent computationBsol: 62.256 Å2
Displacement parametersBiso max: 176.27 Å2 / Biso mean: 74.523 Å2 / Biso min: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-13.542 Å20 Å20 Å2
2--13.542 Å20 Å2
3----27.083 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 0 69 4129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009573
X-RAY DIFFRACTIONc_dihedral_angle_d20.99803
X-RAY DIFFRACTIONc_improper_angle_d1.03943
X-RAY DIFFRACTIONc_angle_deg1.38685
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.3858 131 -
Rwork0.3733 --
obs-2864 81.11 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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