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- PDB-1wwa: NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1wwa
TitleNGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR
ComponentsPROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)
KeywordsTRANSFERASE / TRK RECEPTOR / RECEPTOR TYROSINE KINASE / 3D-DOMAIN SWAPPING
Function / homology
Function and homology information


behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation ...behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / Retrograde neurotrophin signalling / nerve growth factor binding / NGF-independant TRKA activation / sympathetic nervous system development / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / response to axon injury / neuron development / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / axon guidance / receptor protein-tyrosine kinase / kinase binding / positive regulation of neuron projection development / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / learning or memory / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / endosome membrane / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein phosphorylation / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWiesmann, C. / Ultsch, M.H. / Bass, S.H. / De Vos, A.M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of the neurotrophin-binding domain of TrkA, TrkB and TrkC.
Authors: Ultsch, M.H. / Wiesmann, C. / Simmons, L.C. / Henrich, J. / Yang, M. / Reilly, D. / Bass, S.H. / de Vos, A.M.
History
DepositionApr 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: PROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)
Y: PROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)


Theoretical massNumber of molelcules
Total (without water)24,1712
Polymers24,1712
Non-polymers00
Water1,18966
1
X: PROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)


Theoretical massNumber of molelcules
Total (without water)12,0861
Polymers12,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: PROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)


Theoretical massNumber of molelcules
Total (without water)12,0861
Polymers12,0861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29 kcal/mol
Surface area12460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.420, 106.420, 75.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, 0.004, 0.0158), (0.0116, -0.5141, 0.8577), (0.0115, 0.8577, 0.514)
Vector: -17.9648, 96.7557, -54.5886)

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Components

#1: Protein PROTEIN (NERVE GROWTH FACTOR RECEPTOR TRKA)


Mass: 12085.518 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 4.45 Å3/Da / Density % sol: 72.34 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG400011
21 M11NaCl
30.1 Mbis-Tris11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorDate: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 14884 / % possible obs: 95.4 % / Redundancy: 6.5 % / Rsym value: 0.051 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.037 / % possible all: 93
Reflection
*PLUS
Num. measured all: 128530 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.037

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2
Details: THE TWO NCS RELATED MOLECULES UNDERGO 3D-DOMAIN SWAPPING, SUCH THAT STRAND A OF MOLECULE ONE REPLACES STRAND A OF MOLECULE 2 AND VICE VERSA.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 659 4.3 %RANDOM
Rwork0.207 ---
obs-1404 91.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.72 Å20 Å20 Å2
2--12.72 Å20 Å2
3----24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 0 66 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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_it2.2251.5
X-RAY DIFFRACTIONx_mcangle_it3.7442.5
X-RAY DIFFRACTIONx_scbond_it4.1232.5
X-RAY DIFFRACTIONx_scangle_it5.8733
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.409 67 4.5 %
Rwork0.377 1465 -
obs--91.1 %

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