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- PDB-1bm2: GRB2-SH2 DOMAIN IN COMPLEX WITH CYCLO-[N-ALPHA-ACETYL-L-THI ALYSY... -

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Basic information

Entry
Database: PDB / ID: 1bm2
TitleGRB2-SH2 DOMAIN IN COMPLEX WITH CYCLO-[N-ALPHA-ACETYL-L-THI ALYSYL-O-PHOSPHOTYROSYL-VALYL-ASPARAGYL-VALYL-PROLYL] (PKF273-791)
Components
  • PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2)
  • PROTEIN (PKF273-791)
KeywordsHORMONE/GROWTH FACTOR / SH2 DOMAIN / SIGNAL TRANSDUCTION / ADAPTOR PROTEIN / RAS PATHWAY / CYCLIC PEPTIDE / HORMONE-GROWTH FACTOR 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 / : / ERBB2 signaling pathway / entry of bacterium into host cell / branching involved in labyrinthine layer morphogenesis ...: / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / ERBB2 signaling pathway / entry of bacterium into host cell / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / membrane organization / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / interleukin-15-mediated signaling pathway / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of Ras protein signal transduction / 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 / leukocyte migration / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of epidermal growth factor receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / Fc-epsilon receptor signaling pathway / regulation of MAPK cascade / neurotrophin TRK receptor signaling pathway / 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 / T cell costimulation / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / viral process / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRondeau, J.M. / Zurini, M.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Structural and conformational requirements for high-affinity binding to the SH2 domain of Grb2(1).
Authors: Ettmayer, P. / France, D. / Gounarides, J. / Jarosinski, M. / Martin, M.S. / Rondeau, J.M. / Sabio, M. / Topiol, S. / Weidmann, B. / Zurini, M. / Bair, K.W.
History
DepositionJul 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 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: PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2)
L: PROTEIN (PKF273-791)


Theoretical massNumber of molelcules
Total (without water)14,4202
Polymers14,4202
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area6000 Å2
MethodPISA
2
A: PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2)
L: PROTEIN (PKF273-791)

A: PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2)
L: PROTEIN (PKF273-791)


Theoretical massNumber of molelcules
Total (without water)28,8414
Polymers28,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3930 Å2
ΔGint-32 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.780, 83.780, 31.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-179-

HOH

21A-199-

HOH

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Components

#1: Protein PROTEIN (GROWTH FACTOR RECEPTOR BOUND PROTEIN 2) / GRB2


Mass: 13577.362 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: GRB2 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): PLYSS / References: UniProt: GRB2_HUMAN, UniProt: P62993*PLUS
#2: Protein/peptide PROTEIN (PKF273-791) / CYCLO-[N-ALPHA-ACETYL-L-THIALYSYL-O-PHOSPHOTYROSYL -VALYL-ASPARAGYL-VALYL- PROLYL]


Mass: 842.896 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACE: N-TERMINAL ACETYL GROUP PTR: L-PHOSPHOTYROSINE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7
Details: PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 30% SATURATED AMMONIUM SULFATE, 100MM SODIUM HEPES PH 7.0, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
2100 mM1dropNaCl
30.02 %1dropNaN3
430 %ammonium sulfate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. obs: 7262 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.1 / % possible all: 96.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMB

1bmb


Resolution: 2.1→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.232 738 10.3 %RANDOM
Rwork0.197 ---
obs0.197 7184 94.5 %-
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 0 70 945
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.711.5
X-RAY DIFFRACTIONx_mcangle_it4.242
X-RAY DIFFRACTIONx_scbond_it4.722
X-RAY DIFFRACTIONx_scangle_it7.362.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 112 9.4 %
Rwork0.281 1078 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARWATER.TOP
X-RAY DIFFRACTION3PO4.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.281

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