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- PDB-1nrv: Crystal structure of the SH2 domain of Grb10 -

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Basic information

Entry
Database: PDB / ID: 1nrv
TitleCrystal structure of the SH2 domain of Grb10
ComponentsGrowth factor receptor-bound protein 10
KeywordsSIGNALING PROTEIN / DIMER
Function / homology
Function and homology information


vascular associated smooth muscle cell migration / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of glycogen biosynthetic process / negative regulation of D-glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / IRS activation / negative regulation of Wnt signaling pathway / RET signaling / positive regulation of phosphorylation / Signal attenuation ...vascular associated smooth muscle cell migration / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of glycogen biosynthetic process / negative regulation of D-glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / IRS activation / negative regulation of Wnt signaling pathway / RET signaling / positive regulation of phosphorylation / Signal attenuation / ERK1 and ERK2 cascade / FLT3 Signaling / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / insulin receptor binding / Signaling by SCF-KIT / response to insulin / insulin receptor signaling pathway / signaling receptor complex adaptor activity / positive regulation of cold-induced thermogenesis / gene expression / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
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 / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / SH2 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 / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / SH2 domain / SHC Adaptor Protein / PH domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStein, E.G. / Hubbard, S.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural basis for dimerization of the Grb10 Src homology 2 domain. Implications for ligand specificity.
Authors: Stein, E.G. / Ghirlando, R. / Hubbard, S.R.
History
DepositionJan 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 10
B: Growth factor receptor-bound protein 10


Theoretical massNumber of molelcules
Total (without water)24,7222
Polymers24,7222
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.82, 49.04, 79.61
Angle α, β, γ (deg.)90.00, 96.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL ASSEMBLY IS THE DIMER IN THE ASYMMETRIC UNIT.

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Components

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


Mass: 12361.202 Da / Num. of mol.: 2 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB10 OR GRBIR OR KIAA0207 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13322
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.17 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
220 mMHEPES1droppH7.5
3100 mM1dropNaCl
410 %PEG80001reservoir
5100 mM1reservoirpH7.5
65 mMTCEP1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 27261 / Num. obs: 26168 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.5
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.37 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 74325
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A81

1a81


Resolution: 1.65→28.63 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1210 -RANDOM
Rwork0.224 ---
all0.225 25051 --
obs0.224 23841 94.3 %-
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-0.79 Å2
2--0.11 Å20 Å2
3----1.76 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 0 179 1843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.25
X-RAY DIFFRACTIONc_mcangle_it1.9
X-RAY DIFFRACTIONc_scbond_it2.24
X-RAY DIFFRACTIONc_scangle_it3.34
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.259 167 -
Rwork0.258 --
obs-3331 79 %
Refinement
*PLUS
Lowest resolution: 30.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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