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- PDB-3m7f: Crystal structure of the Nedd4 C2/Grb10 SH2 complex -

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Basic information

Entry
Database: PDB / ID: 3m7f
TitleCrystal structure of the Nedd4 C2/Grb10 SH2 complex
Components
  • E3 ubiquitin-protein ligase NEDD4
  • Growth factor receptor-bound protein 10
KeywordsSIGNALING PROTEIN/LIGASE / Nedd4 / C2 domain / Grb10 / SH2 domain / Phosphoprotein / Ligase / Ubl conjugation pathway / SIGNALING PROTEIN-LIGASE complex
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / FLT3 Signaling / positive regulation of nucleocytoplasmic transport / Regulation of PTEN localization / Downregulation of ERBB4 signaling / IRS activation / Insulin receptor signalling cascade / ISG15 antiviral mechanism / Signal attenuation / Signaling by SCF-KIT ...formation of structure involved in a symbiotic process / FLT3 Signaling / positive regulation of nucleocytoplasmic transport / Regulation of PTEN localization / Downregulation of ERBB4 signaling / IRS activation / Insulin receptor signalling cascade / ISG15 antiviral mechanism / Signal attenuation / Signaling by SCF-KIT / vascular associated smooth muscle cell migration / Regulation of PTEN stability and activity / negative regulation of sodium ion transport / nuclear receptor-mediated glucocorticoid signaling pathway / viral budding / negative regulation of potassium ion export across plasma membrane / endocardial cushion development / negative regulation of glycogen biosynthetic process / phosphothreonine residue binding / negative regulation of D-glucose import / RET signaling / receptor catabolic process / protein targeting to lysosome / potassium channel inhibitor activity / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / sodium channel inhibitor activity / proline-rich region binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / RNA polymerase binding / blood vessel morphogenesis / beta-2 adrenergic receptor binding / regulation of dendrite morphogenesis / negative regulation of vascular endothelial growth factor receptor signaling pathway / sodium ion transport / neuromuscular junction development / regulation of synapse organization / negative regulation of Wnt signaling pathway / outflow tract morphogenesis / protein K63-linked ubiquitination / phosphoserine residue binding / protein monoubiquitination / ubiquitin ligase complex / postsynaptic cytosol / progesterone receptor signaling pathway / ERK1 and ERK2 cascade / phosphotyrosine residue binding / ionotropic glutamate receptor binding / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor signaling pathway / T cell activation / ubiquitin binding / regulation of membrane potential / insulin receptor binding / establishment of localization in cell / receptor internalization / neuron projection development / positive regulation of protein catabolic process / cellular response to UV / ubiquitin protein ligase activity / signaling receptor complex adaptor activity / positive regulation of cold-induced thermogenesis / ubiquitin-dependent protein catabolic process / cell cortex / protein-macromolecule adaptor activity / adaptive immune response / gene expression / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / protein-containing complex / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Grb10, SH2 / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / E3 ubiquitin-protein ligase, SMURF1 type / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...Grb10, SH2 / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / E3 ubiquitin-protein ligase, SMURF1 type / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / SH2 domain / SHC Adaptor Protein / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4 / Growth factor receptor-bound protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, Q. / Szebenyi, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis for the Interaction between the Growth Factor-binding Protein GRB10 and the E3 Ubiquitin Ligase NEDD4.
Authors: Huang, Q. / Szebenyi, D.M.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Growth factor receptor-bound protein 10
B: E3 ubiquitin-protein ligase NEDD4


Theoretical massNumber of molelcules
Total (without water)32,9842
Polymers32,9842
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-4 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.163, 70.086, 86.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Growth factor receptor-bound protein 10 / GRB10 adapter protein / Maternally expressed gene 1 protein


Mass: 12644.569 Da / Num. of mol.: 1 / Fragment: UNP residues 514-621, SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Grb10, Kiaa0093, Meg1, Nedd-4, Nedd4, Nedd4a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q60760, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein E3 ubiquitin-protein ligase NEDD4 / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4


Mass: 20339.244 Da / Num. of mol.: 1 / Fragment: UNP residues 71-246, C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Grb10, Kiaa0093, Meg1, Nedd-4, Nedd4, Nedd4a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P46935, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE AT POSITION 583 WAS IDENTIFIED AS SER BASED ON THE ELECTRON DENSITY

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.5
Details: crystallization in 35% MPD, pH 6.5, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 28, 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21866 / Redundancy: 6.5 % / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1NRV AND 3B7Y

1nrv

3b7y


Resolution: 2→43.123 Å / SU ML: 0.25 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1081 5.15 %
Rwork0.1925 --
obs0.1945 20973 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.194 Å2 / ksol: 0.359 e/Å3
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→43.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 0 141 2126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062055
X-RAY DIFFRACTIONf_angle_d1.0572772
X-RAY DIFFRACTIONf_dihedral_angle_d17.612759
X-RAY DIFFRACTIONf_chiral_restr0.077305
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.09270.23951290.20472163X-RAY DIFFRACTION85
2.0927-2.20310.27911210.1922346X-RAY DIFFRACTION92
2.2031-2.34110.26221330.20022429X-RAY DIFFRACTION95
2.3411-2.52180.29171260.20542481X-RAY DIFFRACTION97
2.5218-2.77560.26611360.20622547X-RAY DIFFRACTION98
2.7756-3.17710.24381510.20482575X-RAY DIFFRACTION99
3.1771-4.00240.21371270.16712647X-RAY DIFFRACTION100
4.0024-43.1330.19861580.18622704X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.5699 Å / Origin y: 5.1861 Å / Origin z: 6.4036 Å
111213212223313233
T0.2243 Å20.0074 Å20.0142 Å2-0.2038 Å20.0029 Å2--0.2334 Å2
L1.9337 °2-0.0547 °21.5702 °2-0.8154 °2-0.1361 °2--2.0747 °2
S-0.0099 Å °-0.0891 Å °-0.0584 Å °0.149 Å °-0.0141 Å °0.0529 Å °-0.0321 Å °-0.0148 Å °-0 Å °
Refinement TLS groupSelection details: all

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