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- PDB-1tze: SIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR, GRB2 SH2 DOMAIN COMPLE... -

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Entry
Database: PDB / ID: 1tze
TitleSIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR, GRB2 SH2 DOMAIN COMPLEXED WITH PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2 (KFPPYVNC-NH2)
Components
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
  • PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / SIGNAL TRANSDUCTION ADAPTOR GROWTH FACTOR BOUND PROTEIN 2 (GRB2) SRC HOMOLOGY 2 DOMAIN (SH2) / PHOSPHOTYROSYL HEPTAPEPTIC LIGAND / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology
Function and homology information


: / : / Regulation of T cell activation by CD28 family / : / Signaling by FGFR3 fusions in cancer / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation ...: / : / Regulation of T cell activation by CD28 family / : / Signaling by FGFR3 fusions in cancer / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / neurotrophin TRKA receptor binding / COP9 signalosome / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / vesicle membrane / Signaling by LTK / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / CD28 dependent Vav1 pathway / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of actin filament polymerization / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / insulin receptor substrate binding / signal transduction in response to DNA damage / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / ephrin receptor binding / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / myelination / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / Downstream signal transduction / GRB2 events in ERBB2 signaling / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to ionizing radiation / B cell receptor signaling pathway
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2 / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRahuel, J. / Grutter, M.G.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Structural basis for specificity of Grb2-SH2 revealed by a novel ligand binding mode.
Authors: Rahuel, J. / Gay, B. / Erdmann, D. / Strauss, A. / Garcia-Echeverria, C. / Furet, P. / Caravatti, G. / Fretz, H. / Schoepfer, J. / Grutter, M.G.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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
E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2


Theoretical massNumber of molelcules
Total (without water)12,3922
Polymers12,3922
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-7 kcal/mol
Surface area6100 Å2
MethodPISA
2
E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2


Theoretical massNumber of molelcules
Total (without water)24,7844
Polymers24,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_776-y+2,-x+2,-z+3/21
Buried area4180 Å2
ΔGint-33 kcal/mol
Surface area10000 Å2
MethodPISA
3
E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2


Theoretical massNumber of molelcules
Total (without water)24,7844
Polymers24,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3470 Å2
ΔGint-18 kcal/mol
Surface area10710 Å2
MethodPISA
4
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)24,7844
Polymers24,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
crystal symmetry operation2_774-x+2,-y+2,z-1/21
crystal symmetry operation7_556y,x,-z+11
Buried area3520 Å2
ΔGint-22 kcal/mol
Surface area10660 Å2
MethodPISA
5
I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

I: PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2

E: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)24,7844
Polymers24,7844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation4_474y-1/2,-x+5/2,z-1/41
crystal symmetry operation5_656-x+3/2,y+1/2,-z+5/41
Buried area3080 Å2
ΔGint-19 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 50.300, 89.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11E-198-

HOH

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Components

#1: Protein GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 / GRB2-SH2


Mass: 11447.027 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN RESIDUES 55 - 152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: GRB2 55-152 / Plasmid: PET-3C / Species (production host): Escherichia coli / Gene (production host): GRB2 55-152 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P29354, UniProt: P62993*PLUS
#2: Protein/peptide PHOSPHOTYROSYL HEPTAPEPTIDE LYS-PRO-PHE-PTYR-VAL-ASN-VAL-NH2


Mass: 945.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-25 mg/mlprotein1drop
21.5 Mammonium phosphate1drop
350 mMsodium cacodylate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 7237 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 45126 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.1→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.203 --
obs0.203 7151 100 %
Displacement parametersBiso mean: 26.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 4 103 1067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.991
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.351
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.926
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.351

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