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- PDB-1sg1: Crystal Structure of the Receptor-Ligand Complex between Nerve Gr... -

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Basic information

Entry
Database: PDB / ID: 1sg1
TitleCrystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the Common Neurotrophin Receptor p75
Components
  • Beta-nerve growth factor
  • Tumor necrosis factor receptor superfamily member 16
KeywordsHORMONE/GROWTH FACTOR/MEMBRANE PROTEIN / Nerve Growth Factor / NGF / p75 / Neurotrophin / common neurotrophin receptor / growth factor receptor / receptor-ligand complex / HORMONE-GROWTH FACTOR-MEMBRANE PROTEIN COMPLEX
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 / NFG and proNGF binds to p75NTR / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / death receptor activity / detection of temperature stimulus ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NFG and proNGF binds to p75NTR / 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 / Ceramide signalling / nerve growth factor receptor binding / positive regulation of odontogenesis of dentin-containing tooth / preprotein binding / negative regulation of hair follicle development / NGF processing / positive regulation of synaptic transmission, cholinergic / positive regulation of neuron maturation / TRKA activation by NGF / negative regulation of fibroblast growth factor receptor signaling pathway / PLC-gamma1 signalling / Signalling to STAT3 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / negative regulation of dendritic spine development / metalloendopeptidase inhibitor activity / p75NTR negatively regulates cell cycle via SC1 / nerve growth factor signaling pathway / nerve growth factor binding / nerve development / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / Axonal growth stimulation / NADE modulates death signalling / regulation of neurotransmitter secretion / positive regulation of collateral sprouting / positive regulation of myelination / peripheral nervous system development / Signalling to p38 via RIT and RIN / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase activator activity / ARMS-mediated activation / 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 / PI3K/AKT activation / negative regulation of mitochondrial depolarization / regulation of reactive oxygen species metabolic process / hair follicle morphogenesis / neuronal cell body membrane / Frs2-mediated activation / NRAGE signals death through JNK / 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 / hair follicle development / positive regulation of excitatory postsynaptic potential / Signalling to RAS / positive regulation of synaptic transmission, glutamatergic / positive regulation of axon extension / coreceptor activity / Rho protein signal transduction / neuron projection morphogenesis / extrinsic apoptotic signaling pathway / 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 / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of cell migration / negative regulation of angiogenesis / central nervous system development / endosome lumen / positive regulation of protein ubiquitination / positive regulation of apoptotic signaling pathway / growth factor activity / neuromuscular junction / intracellular protein transport / circadian regulation of gene expression / circadian rhythm / positive regulation of neuron projection development / modulation of chemical synaptic transmission / small GTPase binding / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / Golgi lumen
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 speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsHe, X.L. / Garcia, K.C.
CitationJournal: Science / Year: 2004
Title: Structure of nerve growth factor complexed with the shared neurotrophin receptor p75
Authors: He, X.L. / Garcia, K.C.
History
DepositionFeb 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-nerve growth factor
B: Beta-nerve growth factor
X: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3244
Polymers44,2893
Non-polymers351
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-30 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.692, 91.796, 92.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-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) / Gene: NGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01138
#2: Protein Tumor necrosis factor receptor superfamily member 16 / Low- affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity ...Low- affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity neurotrophin receptor p75NTR


Mass: 17258.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: p75 / Plasmid: pAcGP67A / Production host: unidentified baculovirus / Strain (production host): Tn5 / References: UniProt: P07174
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.71 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 1000, isoproponal, sodium chloride, citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0597 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2003 / Details: null
RadiationMonochromator: null / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 16891 / Num. obs: 16891 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.4 / % possible all: 97.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR
Starting model: part of the structure starts from PDB ENTRY 1WWW

1www


Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 803 -RANDOM
Rwork0.243 ---
all0.245 16891 --
obs0.245 16891 99 %-
Displacement parametersBiso mean: 50.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 1 375 3139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.411 85 -
Rwork0.4 --
obs-1648 97.3 %

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