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- PDB-5gjh: Gads SH2 domain/CD28-derived peptide complex -

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Basic information

Entry
Database: PDB / ID: 5gjh
TitleGads SH2 domain/CD28-derived peptide complex
Components
  • GRB2-related adapter protein 2
  • T-cell-specific surface glycoprotein CD28
KeywordsSIGNALING PROTEIN / Antigens / Phosphopeptides
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / CD28 co-stimulation / positive regulation of CD4-positive, alpha-beta T cell proliferation ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / CD28 co-stimulation / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 dependent Vav1 pathway / positive regulation of interleukin-4 production / CD28 dependent PI3K/Akt signaling / regulation of MAPK cascade / positive regulation of interleukin-10 production / humoral immune response / Generation of second messenger molecules / immunological synapse / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / FLT3 Signaling / positive regulation of interleukin-2 production / phosphotyrosine residue binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of mitotic nuclear division / FCERI mediated Ca+2 mobilization / T cell activation / positive regulation of cytokine production / apoptotic signaling pathway / positive regulation of translation / FCERI mediated MAPK activation / Signaling by SCF-KIT / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Aberrant PI3K in Cancer / DAP12 signaling / PIP3 activates AKT signaling / cell-cell signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Ras protein signal transduction / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / endosome / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRAP2, C-terminal SH3 domain / T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / Immunoglobulin V-Type / SH2 domain ...GRAP2, C-terminal SH3 domain / T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / Immunoglobulin V-Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Immunoglobulin V-set domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GRB2-related adapter protein 2 / T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsInaba, S. / Numoto, N. / Morii, H. / Ogawa, S. / Ikura, T. / Abe, R. / Ito, N. / Oda, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
Authors: Inaba, S. / Numoto, N. / Ogawa, S. / Morii, H. / Ikura, T. / Abe, R. / Ito, N. / Oda, M.
History
DepositionJun 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Nov 8, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB2-related adapter protein 2
B: T-cell-specific surface glycoprotein CD28
C: GRB2-related adapter protein 2
D: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)25,8434
Polymers25,8434
Non-polymers00
Water4,450247
1
A: GRB2-related adapter protein 2
B: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)12,9212
Polymers12,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area6200 Å2
MethodPISA
2
C: GRB2-related adapter protein 2
D: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)12,9212
Polymers12,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-10 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.602, 53.338, 108.302
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 GRB2-related adapter protein 2 / Adapter protein GRID / GRB-2-like protein / GRB2L / GRBLG / GRBX / Grf40 adapter protein / Grf-40 / ...Adapter protein GRID / GRB-2-like protein / GRB2L / GRBLG / GRBX / Grf40 adapter protein / Grf-40 / Growth factor receptor-binding protein / Hematopoietic cell-associated adapter protein GrpL / P38 / Protein GADS / SH3-SH2-SH3 adapter Mona


Mass: 11883.263 Da / Num. of mol.: 2 / Fragment: UNP residues 58-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRAP2, GADS, GRB2L, GRID / Plasmid: pGEX-4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75791
#2: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 1038.047 Da / Num. of mol.: 2 / Fragment: UNP residues 189-196 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10747
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES-NaOH, 10% PEG 6000, 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 61484 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.5
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.7 / CC1/2: 0.96 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSMarch 1, 2015data reduction
XDSMarch 1, 2015data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R1Q

1r1q


Resolution: 1.2→47.85 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1695 3114 5.07 %
Rwork0.1484 --
obs0.1494 61433 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 0 247 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131891
X-RAY DIFFRACTIONf_angle_d1.5912563
X-RAY DIFFRACTIONf_dihedral_angle_d13.102720
X-RAY DIFFRACTIONf_chiral_restr0.113254
X-RAY DIFFRACTIONf_plane_restr0.011334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1995-1.21830.22671440.18992532X-RAY DIFFRACTION97
1.2183-1.23830.20291590.17672622X-RAY DIFFRACTION100
1.2383-1.25960.19951390.16662619X-RAY DIFFRACTION100
1.2596-1.28250.18951300.14842624X-RAY DIFFRACTION100
1.2825-1.30720.16241330.13822640X-RAY DIFFRACTION100
1.3072-1.33390.17071480.1332646X-RAY DIFFRACTION100
1.3339-1.36290.20671430.13132622X-RAY DIFFRACTION100
1.3629-1.39460.16741310.13362626X-RAY DIFFRACTION100
1.3946-1.42950.17351200.12672658X-RAY DIFFRACTION99
1.4295-1.46810.16861380.12352619X-RAY DIFFRACTION99
1.4681-1.51130.15411490.12352559X-RAY DIFFRACTION98
1.5113-1.56010.16431550.11912621X-RAY DIFFRACTION100
1.5601-1.61590.14821420.11762670X-RAY DIFFRACTION100
1.6159-1.68060.16191380.11222673X-RAY DIFFRACTION100
1.6806-1.75710.1521340.1212635X-RAY DIFFRACTION99
1.7571-1.84970.15221600.12762665X-RAY DIFFRACTION100
1.8497-1.96560.17831440.13122672X-RAY DIFFRACTION100
1.9656-2.11740.14191500.13052635X-RAY DIFFRACTION98
2.1174-2.33040.18861370.14262666X-RAY DIFFRACTION99
2.3304-2.66760.191380.16572720X-RAY DIFFRACTION100
2.6676-3.36080.15541430.17012736X-RAY DIFFRACTION99
3.3608-47.88790.17351390.1742859X-RAY DIFFRACTION98

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