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- PDB-4f42: Neurotrophin p75NTR intracellular domain -

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Basic information

Entry
Database: PDB / ID: 4f42
TitleNeurotrophin p75NTR intracellular domain
ComponentsTumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN / death domain / signalling transduction
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / detection of temperature stimulus / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / detection of temperature stimulus / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / dorsal aorta development / p75NTR recruits signalling complexes / death receptor activity / preprotein binding / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / negative regulation of dendritic spine development / nerve development / skeletal muscle cell differentiation / nerve growth factor binding / clathrin-coated endocytic vesicle / positive regulation of myelination / neurotrophin TRKA receptor binding / hair follicle morphogenesis / positive regulation of neural precursor cell proliferation / positive regulation of synaptic transmission, cholinergic / negative regulation of mitochondrial depolarization / regulation of reactive oxygen species metabolic process / skin development / positive regulation of Rho protein signal transduction / neuronal cell body membrane / Rho protein signal transduction / positive regulation of endothelial cell apoptotic process / neuron apoptotic process / extrinsic apoptotic signaling pathway / positive regulation of neuron differentiation / coreceptor activity / positive regulation of synaptic transmission, glutamatergic / negative regulation of angiogenesis / presynaptic modulation of chemical synaptic transmission / positive regulation of apoptotic signaling pathway / intracellular glucose homeostasis / axon guidance / negative regulation of cell migration / positive regulation of fibroblast proliferation / dendrite membrane / positive regulation of excitatory postsynaptic potential / central nervous system development / positive regulation of neuron projection development / circadian regulation of gene expression / negative regulation of neuron projection development / neuromuscular junction / circadian rhythm / positive regulation of protein localization to nucleus / intracellular protein transport / positive regulation of miRNA transcription / small GTPase binding / cellular response to amyloid-beta / cell-cell junction / glucose homeostasis / regulation of gene expression / nuclear envelope / negative regulation of neuron apoptotic process / amyloid-beta binding / response to lipopolysaccharide / growth cone / cellular response to oxidative stress / presynaptic membrane / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / dendritic spine / response to ethanol / positive regulation of MAPK cascade / perikaryon / calmodulin binding / postsynaptic density / positive regulation of apoptotic process / external side of plasma membrane / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / cell surface / mitochondrion / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. ...Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-MERCAPTO-2-NITRO-BENZOIC ACID / Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsQu, Q. / Jiang, T.
CitationJournal: To be Published
Title: Structural insights into the allosteric activation mechanism of p75NTR
Authors: Qu, Q. / Jiang, T.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_ref_seq_dif.details / _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: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0303
Polymers10,6321
Non-polymers3982
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 53.440, 78.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 16 / Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor ...Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor / NGF receptor / p75 ICD


Mass: 10631.906 Da / Num. of mol.: 1 / Fragment: death domain, UNP RESIDUES 334-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ngfr, NM_012610, Tnfrsf16 / Production host: Escherichia coli (E. coli) / References: UniProt: P07174
#2: Chemical ChemComp-MNB / 5-MERCAPTO-2-NITRO-BENZOIC ACID


Mass: 199.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane pH 7.0, 1.2M sodium citrate tribasic dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 4678 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.38→2.48 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NGR

1ngr


Resolution: 2.38→19.6 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25969 229 4.7 %RANDOM
Rwork0.21862 ---
obs0.22053 4678 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.05 Å-
Luzzati d res low-20 Å
Refinement stepCycle: LAST / Resolution: 2.38→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 26 21 700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021691
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0472.006939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.167583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95623.54831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5915111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.685156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021537
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4761.5417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9542663
X-RAY DIFFRACTIONr_scbond_it1.3843274
X-RAY DIFFRACTIONr_scangle_it2.3874.5276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.381→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 15 -
Rwork0.314 338 -
obs--100 %

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