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- PDB-1zfp: GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1zfp
TitleGROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROSYL PENTAPEPTIDE
Components
  • EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
  • GROWTH FACTOR RECEPTOR BINDING PROTEIN
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / SIGNAL TRANSDUCTION / SH2 DOMAIN / PHOSPHOTYROSYL PEPTIDE / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology
Function and homology information


: / 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 / COP9 signalosome ...: / 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 / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / 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 / MET activates RAP1 and RAC1 / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / regulation of MAPK cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / fibroblast growth factor receptor signaling pathway / 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 / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / 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 / signal transduction in response to DNA damage / 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 / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / InlB-mediated entry of Listeria monocytogenes into host cell / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to ionizing radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRahuel, J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structural basis for the high affinity of amino-aromatic SH2 phosphopeptide ligands.
Authors: Rahuel, J. / Garcia-Echeverria, C. / Furet, P. / Strauss, A. / Caravatti, G. / Fretz, H. / Schoepfer, J. / Gay, B.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Aug 9, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3723
Polymers12,3072
Non-polymers651
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-3 kcal/mol
Surface area6120 Å2
MethodPISA
2
E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
hetero molecules

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7446
Polymers24,6144
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_568x,-y+1,-z+31
Buried area3260 Å2
ΔGint-128 kcal/mol
Surface area11590 Å2
MethodPISA
3
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE

I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
hetero molecules

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7446
Polymers24,6144
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558x,-y,-z+31
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation8_458x-1/2,-y+1/2,-z+31
Buried area2130 Å2
ΔGint-119 kcal/mol
Surface area12720 Å2
MethodPISA
4
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE

I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
hetero molecules

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7446
Polymers24,6144
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_559x,-y,-z+41
crystal symmetry operation6_655-x+3/2,-y+1/2,z+1/21
crystal symmetry operation7_648-x+3/2,y-1/2,-z+7/21
Buried area1780 Å2
ΔGint-120 kcal/mol
Surface area13070 Å2
MethodPISA
5
E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
hetero molecules

E: GROWTH FACTOR RECEPTOR BINDING PROTEIN
I: EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7446
Polymers24,6144
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_758-x+2,y,-z+7/21
Buried area4370 Å2
ΔGint-16 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.900, 113.700, 46.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-1-

ZN

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Components

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


Mass: 11443.959 Da / Num. of mol.: 1 / Fragment: SH2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THE PROTEIN WAS EXPRESSED AS A
Gene (production host): THE PROTEIN WAS EXPRESSED AS A FUSION PROTEIN WITH GLUTATHIONE-S-TRANSFERASE (GST) AND CLEAVED USING FACTOR X
Production host: Escherichia coli (E. coli) / References: UniProt: P29354, UniProt: P62993*PLUS
#2: Protein/peptide EPIDERMAL GROWTH FACTOR RECEPTOR-DERIVED PEPTIDE / 2-ABZ-GLU-TYR(PO3H2)-ILE-ASN-GLN-NH2 / WITH 2-ABZ BEING 2-AMINO-BENZOYL


Mass: 862.800 Da / Num. of mol.: 1 / Fragment: 1067-1071
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.73 Å3/Da / Density % sol: 55 % / Description: THE MODEL WAS SUBSTANTIALLY TRUNCATED
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
32 %PEG4001reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 21, 1994
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 12572 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
TFFCmodel building
TNT4-Arefinement
MADNESdata reduction
CCP4data scaling
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCJ (LCK-SH2)

1lcj


Resolution: 1.8→6 Å / σ(F): 0
RfactorNum. reflection% reflection
all0.177 12205 -
obs-12205 99.3 %
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 1 101 909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.011890
X-RAY DIFFRACTIONt_angle_deg1.4251191
X-RAY DIFFRACTIONt_dihedral_angle_d22.481512
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00222
X-RAY DIFFRACTIONt_gen_planes0.01128
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.057
Software
*PLUS
Name: TNT / Version: 4-A / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.481

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