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- PDB-4f44: Neurotrophin p75NTR intracellular domain -

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Basic information

Entry
Database: PDB / ID: 4f44
TitleNeurotrophin p75NTR intracellular domain
ComponentsTumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN / death domain / signaling tranduction
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / death receptor activity / detection of temperature stimulus / dorsal aorta development ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / death receptor activity / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / positive regulation of synaptic transmission, cholinergic / 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 / positive regulation of myelination / nerve development / clathrin-coated endocytic vesicle / nerve growth factor binding / neurotrophin TRKA receptor binding / positive regulation of neural precursor cell proliferation / negative regulation of mitochondrial depolarization / regulation of reactive oxygen species metabolic process / neuronal cell body membrane / hair follicle morphogenesis / skin development / positive regulation of Rho protein signal transduction / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / skeletal muscle cell differentiation / positive regulation of excitatory postsynaptic potential / positive regulation of endothelial cell apoptotic process / hair follicle development / fibroblast growth factor receptor signaling pathway / Rho protein signal transduction / coreceptor activity / extrinsic apoptotic signaling pathway / dendrite membrane / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / positive regulation of synaptic transmission, glutamatergic / axon guidance / negative regulation of angiogenesis / negative regulation of cell migration / central nervous system development / positive regulation of apoptotic signaling pathway / intracellular protein transport / circadian regulation of gene expression / neuromuscular junction / positive regulation of neuron projection development / small GTPase binding / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / circadian rhythm / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / nuclear envelope / glucose homeostasis / cell-cell junction / amyloid-beta binding / presynaptic membrane / negative regulation of neuron projection development / regulation of gene expression / growth cone / cellular response to oxidative stress / fibroblast proliferation / neuron apoptotic process / spermatogenesis / dendritic spine / perikaryon / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / calmodulin binding / postsynaptic density / positive regulation of apoptotic process / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / 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 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Death Domain, Fas / Tumor necrosis factor receptor / nerve growth factor receptor repeats. ...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 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Death Domain, Fas / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Death Domain, Fas / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Refinement description
Revision 1.2Nov 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 16
B: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6624
Polymers21,2642
Non-polymers3982
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.372, 53.372, 73.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 3 - 85 / Label seq-ID: 3 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / Fragment: death domain
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.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane, 1.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Oct 9, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.5011
11K,H,-L20.4989
ReflectionResolution: 2.4→50 Å / Num. all: 9173 / Num. obs: 8699 / % possible obs: 84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 84

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NGR

1ngr


Resolution: 2.4→19.56 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28001 436 4.8 %RANDOM
Rwork0.22792 ---
obs0.23024 8699 99.81 %-
all-9173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 26 53 1377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9861834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3423.54862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89315222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5931512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211032
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_it0.8451.5826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65221316
X-RAY DIFFRACTIONr_scbond_it2.373523
X-RAY DIFFRACTIONr_scangle_it4.1654.5518
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 649 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal0.282
LS refinement shellResolution: 2.399→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 36 -
Rwork0.31 623 -
obs--100 %

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