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- PDB-3hk0: Crystal Structure of the RA and PH Domains of Grb10 -

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Basic information

Entry
Database: PDB / ID: 3hk0
TitleCrystal Structure of the RA and PH Domains of Grb10
ComponentsGrowth factor receptor-bound protein 10
KeywordsSIGNALING PROTEIN / Grb10 / RA / PH / Ras-associating / pleckstrin-homology / adapter protein / Phosphoprotein / SH2 domain
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 phosphorylation / negative regulation of glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / IRS activation / negative regulation of Wnt signaling pathway / RET signaling / Signal attenuation ...vascular associated smooth muscle cell migration / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of glycogen biosynthetic process / negative regulation of phosphorylation / negative regulation of glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / IRS activation / negative regulation of Wnt signaling pathway / RET signaling / Signal attenuation / positive regulation of phosphorylation / negative regulation of insulin receptor signaling pathway / ERK1 and ERK2 cascade / FLT3 Signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / insulin receptor binding / response to insulin / Signaling by SCF-KIT / signaling receptor complex adaptor activity / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / gene expression / protein-containing complex / identical protein binding / 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...Grb10, SH2 / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Ubiquitin-like (UB roll) / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Growth factor receptor-bound protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHubbard, S.R. / Depetris, R.S. / Wu, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14.
Authors: Depetris, R.S. / Wu, J. / Hubbard, S.R.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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: Growth factor receptor-bound protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0593
Polymers59,0012
Non-polymers581
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.875, 48.884, 92.217
Angle α, β, γ (deg.)90.00, 114.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Growth factor receptor-bound protein 10 / GRB10 adapter protein / Insulin receptor-binding protein Grb-IR


Mass: 29500.699 Da / Num. of mol.: 2
Fragment: RAS-associating domain, PH domain, UNP residues 164-415
Mutation: C331S, C232S, C145S, C212S, K270A and E271A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB10, GRBIR, KIAA0207 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q13322
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7
Details: crystals were grown at 17 C in hanging drops containing equal volumes of protein solution and reservoir buffer (~15% PEG 3350, 0.15 M sodium thiocyanate, and 1 mM dithiothreitol (DTT)), pH 7. ...Details: crystals were grown at 17 C in hanging drops containing equal volumes of protein solution and reservoir buffer (~15% PEG 3350, 0.15 M sodium thiocyanate, and 1 mM dithiothreitol (DTT)), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16167 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.667 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3 / Rsym value: 0.323 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 31.32 / SU ML: 0.305 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.094 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27689 821 5.1 %RANDOM
Rwork0.22972 ---
obs0.23221 15264 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.62 Å2
2--1.26 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 3 14 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213602
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9574872
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93523.395162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15815608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2791523
X-RAY DIFFRACTIONr_chiral_restr0.0690.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022691
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21463
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22396
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2591.52221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49323534
X-RAY DIFFRACTIONr_scbond_it0.64931381
X-RAY DIFFRACTIONr_scangle_it1.074.51338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 62 -
Rwork0.361 1093 -
obs--98.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9561-0.35651.22783.07371.41434.83290.0967-0.0158-0.15480.0433-0.1949-0.07980.43430.8280.0981-0.13960.0910.02830.1030.1074-0.172821.271611.51939.0437
27.0010.1369-2.77427.5015-1.04844.8068-0.3872-0.3044-0.38450.5640.18650.95470.2719-0.14420.20070.06340.05260.0927-0.0810.0059-0.0043-0.101124.308528.8764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A109 - 351
2X-RAY DIFFRACTION2B110 - 350

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