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- PDB-1he7: Human Nerve growth factor receptor TrkA -

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Basic information

Entry
Database: PDB / ID: 1he7
TitleHuman Nerve growth factor receptor TrkA
ComponentsHIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
KeywordsTRANSFERASE / TRK-RECEPTOR / STRAND-SWAPPING / NERVE GROWTH FACTOR
Function / homology
Function and homology information


neurotrophin p75 receptor binding / behavioral response to formalin induced pain / olfactory nerve development / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / response to hydrostatic pressure / neurotrophin receptor activity / mechanoreceptor differentiation ...neurotrophin p75 receptor binding / behavioral response to formalin induced pain / olfactory nerve development / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / response to hydrostatic pressure / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / axonogenesis involved in innervation / nerve growth factor binding / Sertoli cell development / Retrograde neurotrophin signalling / sympathetic nervous system development / NGF-independant TRKA activation / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of programmed cell death / positive regulation of Ras protein signal transduction / positive regulation of synapse assembly / PI3K/AKT activation / peptidyl-tyrosine autophosphorylation / Frs2-mediated activation / neurotrophin TRK receptor signaling pathway / detection of temperature stimulus involved in sensory perception of pain / positive regulation of GTPase activity / response to electrical stimulus / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / neuron development / positive regulation of synaptic transmission, glutamatergic / response to axon injury / transmembrane receptor protein tyrosine kinase activity / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / B cell differentiation / response to nutrient levels / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron projection development / circadian rhythm / receptor protein-tyrosine kinase / cellular response to nerve growth factor stimulus / cellular response to nicotine / kinase binding / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome membrane / late endosome / protein autophosphorylation / protein tyrosine kinase activity / neuron apoptotic process / early endosome membrane / spermatogenesis / negative regulation of neuron apoptotic process / learning or memory / early endosome / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / response to xenobiotic stimulus / negative regulation of cell population proliferation / axon / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / 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 Å
AuthorsBanfield, M. / Robertson, A. / Allen, S. / Dando, J. / Tyler, S. / Bennett, G. / Brain, S. / Mason, G. / Holden, P. / Clarke, A. ...Banfield, M. / Robertson, A. / Allen, S. / Dando, J. / Tyler, S. / Bennett, G. / Brain, S. / Mason, G. / Holden, P. / Clarke, A. / Naylor, R. / Wilcock, G. / Brady, R. / Dawbarn, D.
Citation
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure 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.
#2: Journal: Nature / Year: 1999
Title: Crystal Structure of Nerve Growth Factor in Complex with the Ligand-Binding Domain of the Trka Receptor
Authors: Wiesmann, C. / Ultsch, M.H. / Bass, S.H. / De Vos, A.M.
History
DepositionNov 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2001Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0142
Polymers13,9221
Non-polymers921
Water57632
1
A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules

A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0294
Polymers27,8452
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area4770 Å2
ΔGint-42.2 kcal/mol
Surface area13900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)50.854, 50.854, 107.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

DetailsIN DILUTE SOLUTION THE PROTEIN EXISTS AS A MONOMER (NOSTRAND-SWAPPING) AND IS ACTIVE. THE PROTEIN IS INACTIVE INTHE DIMERIC FORM SEEN IN THE CRYSTAL. THE MATRICES FORCONTRUCTING THE DIMER ARE GIVEN IN REMARK 350 BELOW

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Components

#1: Protein HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR / TRK1 TRANSFORMING TYROSINE KINASE PROTEIN / P140-TRKA / TRK-A


Mass: 13922.378 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, SPANS RESIDUES 285-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04629, EC: 2.7.1.112
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE PRESENTED IS OF A STRAND-SWAPPED DIMER. THE SECOND MONOMER IS GENERATED THROUGH ...STRUCTURE PRESENTED IS OF A STRAND-SWAPPED DIMER. THE SECOND MONOMER IS GENERATED THROUGH CRYSTALLOGRAPHIC SYMMETRY. THIS IS NOT THE BIOLOGICALLY ACTIVE FORM OF THE MOLECULE. IT IS ACTIVE ONLY IN THE NON-STRAND SWAPPED STATE.
Has protein modificationY
Sequence detailsTHIS ENTRY IS A SPLICE VARIANT OF THE TRKA_HUMAN (P04629) SEQUENCE IN WHICH RESIDUES 393-398 ARE NOT PRESENT

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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: 1.94 Å3/Da / Density % sol: 32.4 %
Crystal growpH: 4.7
Details: 10 MG/ML PROTEIN + 0.1-0.3M NACL, 0.1M NA-CITRATE, PH 4.6 - 4.8
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
20.1 %sodium azide11
35 mMBis-Tris11
4100-300 mM12NaCl
5100 mMNa citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 43.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WWA

1wwa


Resolution: 2→40 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING ATOMS WERE SET TO ZERO OCCUPANCY AS THEY WERE NOT OBSERVED IN ELECTRON DENSITY, SER A:304 ATOM: OG GLN A:308 ATOMS: CD OE1 NE2 GLU: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflection
Rfree0.276 992 10 %
Rwork0.237 --
obs0.237 10145 99.9 %
Solvent computationBsol: 46.8 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.987 Å20 Å20 Å2
2---8.987 Å20 Å2
3---17.974 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 6 32 876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.7562
X-RAY DIFFRACTIONc_scbond_it2.2382
X-RAY DIFFRACTIONc_scangle_it3.1522.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 123 10 %
Rwork0.254 1109 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3GOL.PAR
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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