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- PDB-3ij2: Ligand-receptor structure -

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Basic information

Entry
Database: PDB / ID: 3ij2
TitleLigand-receptor structure
Components
  • Beta-nerve growth factor
  • Nerve growth factor receptor (TNFR superfamily, member 16)
KeywordsHORMONE/PROTEIN BINDING / Receptor and ligand / Cleavage on pair of basic residues / Disulfide bond / Glycoprotein / Growth factor / Phosphoprotein / Secreted / HORMONE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / Axonal growth stimulation ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / Axonal growth stimulation / Frs2-mediated activation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / death receptor activity / detection of temperature stimulus / dorsal aorta development / positive regulation of neurotrophin TRK receptor signaling pathway / p75NTR recruits signalling complexes / PI3K/AKT activation / ARMS-mediated activation / nerve growth factor receptor binding / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / negative regulation of hair follicle development / positive regulation of neuron maturation / positive regulation of synaptic transmission, cholinergic / Retrograde neurotrophin signalling / negative regulation of fibroblast growth factor receptor signaling pathway / NF-kB is activated and signals survival / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of dendritic spine development / metalloendopeptidase inhibitor activity / neurotrophin binding / nerve growth factor signaling pathway / nerve growth factor binding / nerve development / positive regulation of myelination / clathrin-coated endocytic vesicle / regulation of neurotransmitter secretion / positive regulation of collateral sprouting / neurotrophin TRKA receptor binding / peripheral nervous system development / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of neural precursor cell proliferation / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / negative regulation of mitochondrial depolarization / regulation of neuron differentiation / regulation of reactive oxygen species metabolic process / hair follicle morphogenesis / neuronal cell body membrane / skin development / positive regulation of Rho protein signal transduction / neurotrophin TRK receptor signaling pathway / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / skeletal muscle cell differentiation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endothelial cell apoptotic process / fibroblast growth factor receptor signaling pathway / positive regulation of excitatory postsynaptic potential / hair follicle development / Rho protein signal transduction / positive regulation of axon extension / coreceptor activity / extrinsic apoptotic signaling pathway / neuron projection morphogenesis / positive regulation of protein ubiquitination / extrinsic apoptotic signaling pathway in absence of ligand / sensory perception of pain / dendrite membrane / positive regulation of neuron differentiation / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / axon guidance / negative regulation of angiogenesis / negative regulation of cell migration / positive regulation of apoptotic signaling pathway / central nervous system development / endosome lumen / intracellular protein transport / growth factor activity / 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 / neuron projection development / nuclear envelope / glucose homeostasis / cell-cell junction / regulation of gene expression / negative regulation of neuron projection development
Similarity search - Function
Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Nerve growth factor, beta subunit, mammalian / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor, beta subunit / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like ...Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Nerve growth factor, beta subunit, mammalian / Tumor necrosis factor receptor member 16, transmembrane domain / : / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor, beta subunit / 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 family profile. / Nerve growth factor (NGF or beta-NGF) / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Cystine-knot cytokine / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-nerve growth factor / Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsFeng, D. / Garcia, K.C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular and structural insight into proNGF engagement of p75NTR and sortilin.
Authors: Feng, D. / Kim, T. / Ozkan, E. / Light, M. / Torkin, R. / Teng, K.K. / Hempstead, B.L. / Garcia, K.C.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-nerve growth factor
X: Nerve growth factor receptor (TNFR superfamily, member 16)
B: Beta-nerve growth factor
Y: Nerve growth factor receptor (TNFR superfamily, member 16)


Theoretical massNumber of molelcules
Total (without water)87,8654
Polymers87,8654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-48 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.406, 145.406, 114.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain X and (resseq 2:142 or resseq 148:160 )
211chain Y and (resseq 2:142 or resseq 148:160 )
112chain A and (resseq 9:117 )
212chain B and (resseq 9:117 )

NCS ensembles :
ID
1
2

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Components

#1: Protein Beta-nerve growth factor / Beta-NGF


Mass: 25450.422 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 129-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngf, Ngfb / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01139
#2: Protein Nerve growth factor receptor (TNFR superfamily, member 16)


Mass: 18482.281 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ngfr, RP23-67E18.6-001 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07174
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: 3.97 Å3/Da / Density % sol: 69 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorDate: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.75→50 Å / Num. obs: 14644

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_153refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.75→47.595 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.3 / σ(F): 1.33 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 737 5.04 %
Rwork0.2556 --
obs0.2565 14620 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 117.111 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 167.25 Å2
Baniso -1Baniso -2Baniso -3
1-20.87 Å20 Å2-0 Å2
2--20.87 Å20 Å2
3----41.74 Å2
Refinement stepCycle: LAST / Resolution: 3.75→47.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 0 0 4092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134198
X-RAY DIFFRACTIONf_angle_d1.5685666
X-RAY DIFFRACTIONf_dihedral_angle_d18.5511468
X-RAY DIFFRACTIONf_chiral_restr0.088644
X-RAY DIFFRACTIONf_plane_restr0.005748
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X1119X-RAY DIFFRACTIONPOSITIONAL
12Y1119X-RAY DIFFRACTIONPOSITIONAL0.055
21A854X-RAY DIFFRACTIONPOSITIONAL
22B854X-RAY DIFFRACTIONPOSITIONAL0.155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7503-4.03970.31371700.30132711X-RAY DIFFRACTION100
4.0397-4.4460.26021590.2562719X-RAY DIFFRACTION100
4.446-5.08870.28111350.22212753X-RAY DIFFRACTION100
5.0887-6.40880.26491310.23542814X-RAY DIFFRACTION100
6.4088-47.59910.2611420.25892886X-RAY DIFFRACTION100

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