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- PDB-4xpj: Crystal structure of Nerve growth factor in complex with lysophos... -

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Basic information

Entry
Database: PDB / ID: 4xpj
TitleCrystal structure of Nerve growth factor in complex with lysophosphatidylinositol
ComponentsBeta-nerve growth factor
KeywordsHORMONE / Nerve Growth Factor / LysoPI
Function / homology
Function and homology information


TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / nerve growth factor receptor binding / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / Retrograde neurotrophin signalling / NF-kB is activated and signals survival / metalloendopeptidase inhibitor activity / positive regulation of neuron maturation / nerve growth factor signaling pathway / regulation of neurotransmitter secretion / nerve development / positive regulation of collateral sprouting / peripheral nervous system development / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / regulation of neuron differentiation / positive regulation of DNA binding / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / positive regulation of axon extension / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / sensory perception of pain / positive regulation of neuron differentiation / adult locomotory behavior / neuron projection morphogenesis / positive regulation of protein ubiquitination / endosome lumen / growth factor activity / modulation of chemical synaptic transmission / memory / positive regulation of neuron projection development / circadian rhythm / neuron projection development / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / axon / lipid binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region
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) / Cystine Knot Cytokines, subunit B ...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) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-LPY / Beta-nerve growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsSun, H.L. / Jiang, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The structure of nerve growth factor in complex with lysophosphatidylinositol
Authors: Sun, H.L. / Jiang, T.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5133
Polymers26,9832
Non-polymers5311
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-18 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.689, 96.689, 164.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 13491.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01139
#2: Chemical ChemComp-LPY / (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate / sn-1-tridecanoyl-phosphatidylinositol


Mass: 530.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H43O12P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M imidazole, 1.0 M Na acetate / PH range: 6.3 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 8340 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.58
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EAX

4eax


Resolution: 2.605→37.304 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 414 4.96 %
Rwork0.1952 --
obs0.1987 8340 89.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.605→37.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 35 60 1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091728
X-RAY DIFFRACTIONf_angle_d1.0852332
X-RAY DIFFRACTIONf_dihedral_angle_d16.927605
X-RAY DIFFRACTIONf_chiral_restr0.047272
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6048-2.98150.32431060.22962008X-RAY DIFFRACTION69
2.9815-3.75590.28661430.1972923X-RAY DIFFRACTION100
3.7559-37.30810.24051650.18512995X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -28.0555 Å / Origin y: 4.5736 Å / Origin z: 14.2545 Å
111213212223313233
T0.2385 Å20.0718 Å20.0245 Å2-0.5008 Å2-0.0829 Å2--0.2474 Å2
L3.6369 °20.0132 °2-0.8618 °2-2.0848 °20.5325 °2--1.5829 °2
S-0.1928 Å °-0.1224 Å °0.0249 Å °0.1827 Å °-0.0886 Å °0.5142 Å °-0.0886 Å °-0.5743 Å °0.2215 Å °
Refinement TLS groupSelection details: all

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