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- PDB-1www: NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1www
TitleNGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR
Components
  • PROTEIN (NERVE GROWTH FACTOR)
  • PROTEIN (TRKA RECEPTOR)
KeywordsNERVE GROWTH FACTOR/TRKA COMPLEX / COMPLEX / TRKA RECEPTOR / NERVE GROWTH FACTOR / CYSTEINE KNOT / IMMUNOGLOBULIN LIKE DOMAIN / NERVE GROWTH FACTOR-TRKA COMPLEX COMPLEX
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling ...NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / 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 / p75NTR negatively regulates cell cycle via SC1 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / metalloendopeptidase inhibitor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / positive regulation of collateral sprouting / nerve growth factor binding / NGF-independant TRKA activation / NADE modulates death signalling / sympathetic nervous system development / Signalling to p38 via RIT and RIN / peripheral nervous system development / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / regulation of neuron differentiation / Frs2-mediated activation / NRAGE signals death through JNK / 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 / extrinsic apoptotic signaling pathway via death domain receptors / response to axon injury / neuron development / Signalling to RAS / positive regulation of DNA binding / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / p75NTR recruits signalling complexes / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / neuron projection morphogenesis / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / endosome lumen / axon guidance / growth factor activity / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / memory / kinase binding / positive regulation of neuron projection development / Golgi lumen / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / synaptic vesicle / late endosome / positive regulation of peptidyl-serine phosphorylation / 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 / lipid binding
Similarity search - Function
Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / High affinity nerve growth factor receptor NTRK1 ...Nerve growth factor, beta subunit, mammalian / Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Cystine-knot cytokine / 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 / Ribbon / 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
Beta-nerve growth factor / High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWiesmann, C. / Ultsch, M.H. / De Vos, A.M.
CitationJournal: 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
DepositionMar 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,2464
Polymers49,2464
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-55 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.245, 53.735, 77.101
Angle α, β, γ (deg.)90.00, 107.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.58128, -0.31271, -0.75121), (-0.29055, -0.94211, 0.1673), (-0.76006, 0.121, -0.63849)14.78126, 0.8221, 30.56634
2given(0.56952, -0.31199, -0.76047), (-0.32931, -0.93428, 0.13667), (-0.75313, 0.17259, -0.63483)14.76906, 2.01039, 30.27118

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Components

#1: Protein PROTEIN (NERVE GROWTH FACTOR) / BETA-NGF


Mass: 13515.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01138
#2: Protein PROTEIN (TRKA RECEPTOR)


Mass: 11107.459 Da / Num. of mol.: 2 / Fragment: DOMAIN 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04629
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Description: DATA WERE COLLECTED AT THE ADVANCED LIGHT SOURCE, BERKELEY
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 M1dropNaCl
30.1 Mbicine1drop
424 %PEG33501reservoir
50.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 23361 / % possible obs: 99.8 % / Redundancy: 4 % / Rsym value: 0.071 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rsym value: 0.355 / % possible all: 98.7
Reflection
*PLUS
Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Rmerge(I) obs: 0.355

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BET

1bet


Resolution: 2.2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGOUT / σ(F): 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2282 10 %RANDOM
Rwork0.189 ---
obs-22780 97.25 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 262 3545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.91
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3784 259 9.1 %
Rwork0.283 2391 -
obs--90.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.91
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % reflection Rfree: 9.1 % / Rfactor Rwork: 0.283

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