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- PDB-1fyr: DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 1fyr
TitleDIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE OF THE GRB2-SH2 AC-PYVNV COMPLEX
Components
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
  • HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
KeywordsHORMONE/GROWTH FACTOR / Grb2 / SH2 domain / phosphopeptide / Met / domain swapping / dimerization / HORMONE-GROWTH FACTOR 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 / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity ...: / : / 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 / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / MET interacts with TNS proteins / Co-inhibition by BTLA / endothelial cell morphogenesis / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / semaphorin receptor activity / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / pancreas development / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / vesicle membrane / Sema4D mediated inhibition of cell attachment and migration / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / epidermal growth factor receptor binding / MET activates PTK2 signaling / 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 / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / PI-3K cascade:FGFR1 / positive regulation of actin filament polymerization / endodermal cell differentiation / negative regulation of thrombin-activated receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / semaphorin-plexin signaling pathway / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / 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 / establishment of skin barrier / 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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / MECP2 regulates neuronal receptors and channels / 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
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / SH2 domain / SHC Adaptor Protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / 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: 2.4 Å
AuthorsSchiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C.
CitationJournal: Biochemistry / Year: 2000
Title: Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex.
Authors: Schiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Please note it has not been proven that the domain- swapped dimer has biological significance.

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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: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
D: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
L: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)55,5228
Polymers55,5228
Non-polymers00
Water3,279182
1
A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)27,7614
Polymers27,7614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-45 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
D: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
L: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)27,7614
Polymers27,7614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-43 kcal/mol
Surface area10810 Å2
MethodPISA
3
C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE

D: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
L: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE

A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)55,5228
Polymers55,5228
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-73 kcal/mol
Surface area25260 Å2
MethodPISA
4
A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE

C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
D: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
L: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)55,5228
Polymers55,5228
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_546y,x-1,-z+11
Buried area16100 Å2
ΔGint-106 kcal/mol
Surface area19640 Å2
MethodPISA
5
C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE

A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
I: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)41,6426
Polymers41,6426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation7_546y,x-1,-z+11
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-70 kcal/mol
Surface area17460 Å2
MethodPISA
6
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
J: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE

C: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
D: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
K: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE
L: HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)41,6426
Polymers41,6426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation7_656y+1,x,-z+11
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-67 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.610, 77.610, 183.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer 1 is formed from chain I and chain J related by NCS (physiological role not demonstrated) / Dimer 2 is formed from chain K and chain L related by NCS (physiological role not demonstrated)

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Components

#1: Protein
GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2


Mass: 13281.041 Da / Num. of mol.: 4 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P29354, UniProt: P62993*PLUS
#2: Protein/peptide
HEPATOCYTE GROWTH FACTOR RECEPTOR PEPTIDE


Mass: 599.570 Da / Num. of mol.: 4 / Fragment: RESIDUES 1356-1359 (RESIDUES 0-3 IN COORDINATES) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence occurs naturally in humans.
References: UniProt: P08581
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 11% PEG 3350, 0.5M NaCL, 0.1M MES/NaOH pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
2300 mM1dropNaCl
311 %PEG33501reservoir
4100 mMMES-NaOH1reservoir
50.5 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 22423 / Num. obs: 22423 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.58 Å / Rmerge(I) obs: 0.252 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 140468
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameClassification
AMoREphasing
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GRI

1gri


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1100 5 %RANDOM
Rwork0.217 ---
all0.22 22403 --
obs0.22 22403 98.7 %-
Solvent computationSolvent model: mask / Bsol: 30.84 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å2--
2--4.75 Å2-
3----9.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 182 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.81.5
X-RAY DIFFRACTIONc_mcangle_it1.462
X-RAY DIFFRACTIONc_scbond_it0.842
X-RAY DIFFRACTIONc_scangle_it1.422.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 174 4.8 %
Rwork0.248 3432 -
obs-2030 97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNX / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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