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- PDB-3wa4: Grb2 SH2 domain/CD28-derived peptide complex -

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Basic information

Entry
Database: PDB / ID: 3wa4
TitleGrb2 SH2 domain/CD28-derived peptide complex
Components
  • Growth factor receptor-bound protein 2GRB2
  • T-cell-specific surface glycoprotein CD28
KeywordsSIGNALING PROTEIN / Grb2 SH2 domain
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 / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / 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 ...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 / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / 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 / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / COP9 signalosome / CD28 co-stimulation / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / vesicle membrane / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / MET activates RAP1 and RAC1 / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / positive regulation of interleukin-4 production / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / regulation of MAPK cascade / CD28 dependent PI3K/Akt signaling / positive regulation of interleukin-10 production / GRB2:SOS provides linkage to MAPK signaling for Integrins / humoral immune response / RHOU GTPase cycle / PI3K events in ERBB2 signaling / immunological synapse / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / fibroblast growth factor receptor signaling pathway / signal transduction in response to DNA damage / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / positive regulation of viral genome replication / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / coreceptor activity / MET activates RAS signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / positive regulation of T cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / T cell costimulation / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / T cell activation / positive regulation of interleukin-2 production / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ephrin receptor binding
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / Immunoglobulin V-Type ...T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / 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
ACETIC ACID / : / T-cell-specific surface glycoprotein CD28 / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHigo, K. / Oda, M. / Ito, N.
CitationJournal: Plos One / Year: 2013
Title: High Resolution Crystal Structure of the Grb2 SH2 Domain with a Phosphopeptide Derived from CD28
Authors: Higo, K. / Ikura, T. / Oda, M. / Morii, H. / Takahashi, J. / Abe, R. / Ito, N.
History
DepositionApr 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _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: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5824
Polymers12,4102
Non-polymers1722
Water1,15364
1
A: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5443
Polymers11,3721
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-cell-specific surface glycoprotein CD28


  • defined by author
  • 1.04 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0381
Polymers1,0381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-8 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.010, 59.010, 117.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Growth factor receptor-bound protein 2 / GRB2 / Adapter protein GRB2 / Protein Ash / SH2/SH3 adapter GRB2


Mass: 11371.807 Da / Num. of mol.: 1 / Fragment: SH2 domain, UNP resideus 57-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Production host: Escherichia coli (E. coli) / References: UniProt: P62993
#2: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 1038.047 Da / Num. of mol.: 1 / Fragment: fragment peptide, UNP residues 190-195 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P10747
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 26, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 26431 / Num. obs: 26431 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Redundancy: 20.6 % / Rsym value: 0.057
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 21.2 % / Rsym value: 0.498 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C7I

3c7i


Resolution: 1.35→23.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20868 1317 5 %RANDOM
Rwork0.17553 ---
obs0.17725 25113 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.004 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.19 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 5 64 917
Refine LS restraints
Refine-IDTypeDev idealNumberDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.02896
X-RAY DIFFRACTIONr_bond_other_d0842
X-RAY DIFFRACTIONr_angle_refined_deg2.1061208
X-RAY DIFFRACTIONr_angle_other_deg3.6811930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8151065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.174623.261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44115615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151715
X-RAY DIFFRACTIONr_chiral_restr0.1441220.2
X-RAY DIFFRACTIONr_gen_planes_refined0.014102278.29
X-RAY DIFFRACTIONr_gen_planes_other0.025235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr15.23617383
X-RAY DIFFRACTIONr_sphericity_free24.007215
X-RAY DIFFRACTIONr_sphericity_bonded11.34417595
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 98 -
Rwork0.155 1820 -
obs--98.16 %

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