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- PDB-5nvj: SH3 domain from Mouse cortactin (C 1 2 1 crystal form) -

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Basic information

Entry
Database: PDB / ID: 5nvj
TitleSH3 domain from Mouse cortactin (C 1 2 1 crystal form)
ComponentsSrc substrate cortactin
KeywordsSIGNALING PROTEIN / SH3 domain / cortactin / signaling / cancer / invadopodium
Function / homology
Function and homology information


lamellipodium organization / site of polarized growth / Arp2/3 complex binding / mitotic spindle midzone / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton ...lamellipodium organization / site of polarized growth / Arp2/3 complex binding / mitotic spindle midzone / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton / regulation of actin filament polymerization / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / positive regulation of chemotaxis / focal adhesion assembly / proline-rich region binding / podosome / dendritic spine maintenance / regulation of axon extension / positive regulation of actin filament polymerization / cortical actin cytoskeleton / cortical cytoskeleton / voltage-gated potassium channel complex / clathrin-coated pit / extrinsic apoptotic signaling pathway / ruffle / receptor-mediated endocytosis / neuron projection morphogenesis / cell motility / actin filament / negative regulation of extrinsic apoptotic signaling pathway / intracellular protein transport / actin filament binding / cell migration / cell junction / lamellipodium / cell cortex / actin cytoskeleton organization / postsynapse / dendritic spine / focal adhesion / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / CITRIC ACID / Src substrate cortactin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsTwafra, S. / Dessau, M.
CitationJournal: To Be Published
Title: SH3 domain from Mouse cortactin (C 1 2 1 crystal form)
Authors: Twafra, S. / Gil-Henn, H. / Dessau, M.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 2.0Aug 4, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Src substrate cortactin
B: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1306
Polymers13,6052
Non-polymers5254
Water2,558142
1
A: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2074
Polymers6,8031
Non-polymers4043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9232
Polymers6,8031
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.610, 35.430, 64.300
Angle α, β, γ (deg.)90.000, 135.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-268-

HOH

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Components

#1: Protein Src substrate cortactin


Mass: 6802.532 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q60598
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 1% benzamidine hydrochloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.18→44.7 Å / Num. obs: 40754 / % possible obs: 92.4 % / Redundancy: 1.99 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 9.98
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 3626 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X69

1x69


Resolution: 1.18→44.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.201 --
Rwork0.189 --
obs-36051 92.4 %
Displacement parametersBiso max: 99.73 Å2 / Biso mean: 23.0236 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: LAST / Resolution: 1.18→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 37 142 1136

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