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- PDB-8dgo: Growth Factor Receptor-Bound Protein 2 (Grb2) bound to phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 8dgo
TitleGrowth Factor Receptor-Bound Protein 2 (Grb2) bound to phosphorylated PEAK3 (pY24) peptide
Components
  • Growth factor receptor bound protein 2
  • Phosphorylated PEAK3 (pY24) peptide
KeywordsSIGNALING PROTEIN / SH2 domain
Function / homology
Function and homology information


endosome / Golgi apparatus / nucleus
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Growth factor receptor bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoy, M.J. / Hardy, J.M. / Lucet, I.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1144149 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling.
Authors: Roy, M.J. / Surudoi, M.G. / Kropp, A. / Hou, J. / Dai, W. / Hardy, J.M. / Liang, L.Y. / Cotton, T.R. / Lechtenberg, B.C. / Dite, T.A. / Ma, X. / Daly, R.J. / Patel, O. / Lucet, I.S.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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 2
B: Growth factor receptor bound protein 2
C: Phosphorylated PEAK3 (pY24) peptide


Theoretical massNumber of molelcules
Total (without water)51,6733
Polymers51,6733
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC experiments confirm binding of the PEAK3 (pY24) peptide to Grb2 (1:1 stoichiometry).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-11 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.310, 89.310, 94.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Growth factor receptor bound protein 2 / Macaca fascicularis brain cDNA clone: QmoA-10218 / similar to human growth factor receptor-bound ...Macaca fascicularis brain cDNA clone: QmoA-10218 / similar to human growth factor receptor-bound protein 2 (GRB2) / transcript variant 1 / mRNA / RefSeq: NM_002086.3


Mass: 25384.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q2PG25
#2: Protein/peptide Phosphorylated PEAK3 (pY24) peptide


Mass: 903.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.7 M sodium acetate pH 8.0, 10 % (v/v) glycerol, with 1 mM PEAK3 (pY24) peptide

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→47.41 Å / Num. obs: 32908 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Net I/σ(I): 11.8 / Num. measured all: 226651
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.386.41.6781941730520.4240.7071.8241.294.5
8.91-47.416.60.05839295930.9960.0240.0633298.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDS20161205data reduction
Aimless0.5.21data scaling
PHASER2.8.3phasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GRI

1gri


Resolution: 2.3→41.88 Å / SU ML: 0.3869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 1541 4.69 %
Rwork0.1788 31310 -
obs0.1809 32851 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 0 110 3674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813670
X-RAY DIFFRACTIONf_angle_d0.98514964
X-RAY DIFFRACTIONf_chiral_restr0.0595498
X-RAY DIFFRACTIONf_plane_restr0.0085657
X-RAY DIFFRACTIONf_dihedral_angle_d10.4773481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.4171280.34872660X-RAY DIFFRACTION93.37
2.38-2.460.3911170.31232874X-RAY DIFFRACTION99.93
2.46-2.560.31161310.26732853X-RAY DIFFRACTION99.97
2.56-2.680.28231420.25772829X-RAY DIFFRACTION100
2.68-2.820.29251350.26112886X-RAY DIFFRACTION100
2.82-2.990.30731490.26492843X-RAY DIFFRACTION99.97
2.99-3.220.27721510.21982856X-RAY DIFFRACTION100
3.22-3.550.24441380.19182858X-RAY DIFFRACTION99.97
3.55-4.060.22221770.14942843X-RAY DIFFRACTION100
4.06-5.120.16791760.12932837X-RAY DIFFRACTION99.97
5.12-41.880.162970.14342971X-RAY DIFFRACTION99.77
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)
16.344056308844.779552676151.889380128184.241327325132.91227654168.122411341020.247455936042-1.300635431921.327283930480.378965666313-0.5123397632280.668759196338-0.4155014801520.1579745589690.245593919880.480832938577-0.09701616216540.02569322203340.835147511619-0.2321417858470.65750892703625.6883951044-15.073789384715.9705168332
22.4932044060.390870748494-0.8885037900775.99286088596-2.50279121474.76085088097-0.0687702568337-0.53413306415-0.1031096128240.497879036148-0.1406468330090.06392074120820.2992358407730.119296586330.2025002931070.4420810917090.02139334920670.05523375768370.557654547356-0.05348597402140.46059708867614.2486616036-32.831798094610.7865238032
30.737408267092-0.2348287244690.7731880902223.56164420851-4.695905102936.47457173804-0.970953491071-0.264293291648-0.6846019029931.45246690541-0.462797911527-0.9980147196420.4187992971031.181409315321.281368759071.154141332960.131121857809-0.1059198209960.8328611936510.2091985659111.1316696755712.7723357911-55.648777724619.919650263
48.78405457047-1.093885514681.588884731764.889378392091.55313592197.417592223350.1573767280560.497872585485-0.44889063671-0.199394718107-0.3173390225280.6748592531930.521606664029-0.2311532012790.1661748127470.6262463188630.00380768437133-0.02209265303320.46413701189-0.07229983734580.4737521636358.72405276304-45.4605629755-13.7296153716
52.932461955911.39744922598-1.707128567633.61583930035-1.351767103493.33691211619-0.2257734987180.166404612629-0.0326779031413-0.4737330794240.0684819395398-0.1006898129670.185810588992-0.11254398910.1818919268840.4568898807790.0261577135521-0.001064952933620.405343946671-0.03555892867190.43725686533216.8698996802-25.9190966426-8.74440091967
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 0 through 55 )BB0 - 551 - 56
22chain 'B' and (resid 56 through 217 )BB56 - 21757 - 218
33chain 'C' and (resid 25 through 27 )CC25 - 273 - 5
44chain 'A' and (resid -1 through 55 )AA-1 - 551 - 57
55chain 'A' and (resid 56 through 217 )AA56 - 21758 - 219

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