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- PDB-1cj1: GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1cj1
TitleGROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE
ComponentsPROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / SH2 DOMAIN / PHOSPHOTYROSINE
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling / 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 / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / 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 / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / signal transduction in response to DNA damage / fibroblast growth factor receptor signaling pathway / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signalling to RAS / GAB1 signalosome / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / ephrin receptor binding / Signaling by FGFR2 in disease / phosphotyrosine residue binding / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / 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 / cellular response to ionizing radiation / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / T cell activation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / EGFR downregulation / Spry regulation of FGF signaling
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
Chem-C78 / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRahuel, J.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Structure-based design, synthesis, and X-ray crystallography of a high-affinity antagonist of the Grb2-SH2 domain containing an asparagine mimetic.
Authors: Furet, P. / Garcia-Echeverria, C. / Gay, B. / Schoepfer, J. / Zeller, M. / Rahuel, J.
History
DepositionApr 21, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
B: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
C: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
D: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
E: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
F: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
G: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
H: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
I: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
J: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
K: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
L: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,15624
Polymers134,24012
Non-polymers7,91612
Water724
1
A: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
B: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-14 kcal/mol
Surface area9240 Å2
MethodPISA
2
C: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
D: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-15 kcal/mol
Surface area9270 Å2
MethodPISA
3
E: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
F: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-15 kcal/mol
Surface area9250 Å2
MethodPISA
4
G: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
H: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-13 kcal/mol
Surface area9220 Å2
MethodPISA
5
I: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
J: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-13 kcal/mol
Surface area9240 Å2
MethodPISA
6
K: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
L: PROTEIN (GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6934
Polymers22,3732
Non-polymers1,3192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-15 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 93.300, 232.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99891, 0.00247, 0.0467), (0.01363, -0.93987, 0.34126), (0.04474, 0.34152, 0.93881)36.80974, -2.01992, -0.39147
2given(0.99694, 0.04097, 0.06655), (0.05501, 0.23685, -0.96999), (-0.0555, 0.97068, 0.23388)-15.46572, 86.56638, 65.24052
3given(-0.99721, -0.00737, 0.07427), (-0.05748, -0.55886, -0.82727), (0.0476, -0.82923, 0.55688)22.06258, 87.7924, 61.38384
4given(0.99941, 0.02013, -0.028), (-0.0339, 0.42539, -0.90437), (-0.00629, 0.90478, 0.42582)-11.61088, 72.3908, 173.36424
5given(-0.99913, -0.03445, -0.02351), (0.04128, -0.73622, -0.67548), (0.00596, -0.67586, 0.737)26.13474, 69.36281, 170.56409
6given(0.99863, 0.0335, 0.04009), (-0.0025, 0.79713, -0.6038), (-0.05218, 0.60288, 0.79612)-4.10425, 62.37164, 107.0884
7given(-0.9975, -0.00863, 0.07018), (-0.01154, -0.95932, -0.28208), (0.06976, -0.28218, 0.95682)33.15971, 60.56376, 103.74034
8given(0.99869, 0.02488, 0.04473), (0.00695, 0.79982, -0.60019), (-0.05071, 0.59972, 0.7986)-12.35461, 15.98218, 177.28513
9given(-0.99718, 0.00184, 0.07503), (-0.02517, -0.95002, -0.31116), (0.07071, -0.31217, 0.94739)24.67863, 15.2609, 174.3291
10given(-0.9999, 0.00227, -0.01417), (0.01324, -0.23385, -0.97218), (-0.00552, -0.97227, 0.2338)23.283, 39.90322, 91.12155
11given(0.99991, -0.00167, 0.01302), (0.01258, -0.16259, -0.98661), (0.00376, 0.98669, -0.16256)-15.07632, 40.04492, 93.91479
DetailsTHE ASYMMETRIC UNIT CONSISTS OF 12 COPIES OF MOLECULE A. AUTHOR ORIGINALLY PROVIDED COORDINATES FOR ONE COPY OF THE MOLECULE A AND 11 NCS MATRICES FOR THIS FILE SINCE STRICT NCS WERE USED DURING REFINEMENT. The PDB USED 11 MATRICES GIVEN TO GENERATE OTHER 11 COPIES OF THE MOLECULE FOR THIS FILE.

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Components

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


Mass: 11186.650 Da / Num. of mol.: 12 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH PHOSPHOTYROSYL DERIVATIVE / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62993
#2: Chemical
ChemComp-C78 / [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER


Mass: 659.667 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H42N5O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.83 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-10.4 mg/mlprotein1drop
30.1 MHEPES1reservoir
41.4 Msodium acetate1reservoir
2compound 2b1drop5 fold molar excess

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30.12 Å / Num. obs: 31921 / % possible obs: 96 % / Redundancy: 3.91 % / Rsym value: 20 / Net I/σ(I): 8.46
Reflection shellResolution: 3→3.5 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.27 / Rsym value: 41 / % possible all: 96
Reflection
*PLUS
Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1Frefinement
XDSdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TZE

1tze


Resolution: 3→31 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1534 4.8 %RANDOM
Rwork0.3047 ---
obs-30979 91.8 %-
Displacement parametersBiso mean: 25.15 Å2
Refinement stepCycle: LAST / Resolution: 3→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9504 0 552 4 10060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.027
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_deg2.536
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.63
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.5122 189 5.4 %
Rwork0.4307 3331 -
obs--96.6 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.305
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.63
LS refinement shell
*PLUS
% reflection Rfree: 5.4 %

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