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- PDB-4eax: Mouse NGF in complex with Lyso-PS -

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Basic information

Entry
Database: PDB / ID: 4eax
TitleMouse NGF in complex with Lyso-PS
ComponentsBeta-nerve growth factor
KeywordsHORMONE / Lyso-PS / phospholipid
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 / cell surface receptor protein tyrosine kinase signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein autophosphorylation / sensory perception of pain / positive regulation of neuron differentiation / neuron projection morphogenesis / adult locomotory behavior / 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-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) / Cystine Knot Cytokines, subunit B ...Nerve growth factor, beta subunit, mammalian / 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) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-S12 / Beta-nerve growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, T. / Tong, Q.
CitationJournal: Faseb J. / Year: 2012
Title: Structural and functional insights into lipid-bound nerve growth factors
Authors: Tong, Q. / Wang, F. / Zhou, H.Z. / Sun, H.L. / Song, H. / Shu, Y.Y. / Gong, Y. / Zhang, W.T. / Cai, T.X. / Yang, F.Q. / Tang, J. / Jiang, T.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: 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_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 1.2Oct 30, 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: Beta-nerve growth factor
B: Beta-nerve growth factor
C: Beta-nerve growth factor
D: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0126
Polymers53,9654
Non-polymers1,0472
Water1,08160
1
A: Beta-nerve growth factor
B: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5063
Polymers26,9832
Non-polymers5241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-17 kcal/mol
Surface area12630 Å2
MethodPISA
2
C: Beta-nerve growth factor
D: Beta-nerve growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5063
Polymers26,9832
Non-polymers5241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-19 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.529, 96.529, 163.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 13491.255 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01139
#2: Chemical ChemComp-S12 / O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine / 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine


Type: L-peptide linking / Mass: 523.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46NO9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11.009
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 8, 2010
RAYONIX MX225HE2CCDJan 31, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NI MIRRORSINGLE WAVELENGTHMx-ray1
2NI MIRRORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
211
ReflectionResolution: 2.3→40.5 Å / Num. all: 25278 / Num. obs: 24969 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 46.03 Å2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2240 / % possible all: 89.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTG

1btg


Resolution: 2.3→40.5 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7797 / SU ML: 0.33 / σ(F): 0.13 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 1215 5.12 %RANDOM
Rwork0.2187 ---
all0.2228 25278 --
obs0.2208 23751 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.217 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 126.72 Å2 / Biso mean: 58.4532 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-5.4299 Å2-0 Å2-0 Å2
2--5.4299 Å20 Å2
3----10.8598 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 54 60 3498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013545
X-RAY DIFFRACTIONf_angle_d1.2344778
X-RAY DIFFRACTIONf_chiral_restr0.078551
X-RAY DIFFRACTIONf_plane_restr0.004598
X-RAY DIFFRACTIONf_dihedral_angle_d18.971250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.39220.291100.25982011212176
2.3922-2.5010.36461130.25752346245987
2.501-2.63290.31821410.25062466260793
2.6329-2.79780.33341310.26272530266195
2.7978-3.01370.33871480.25582621276998
3.0137-3.31690.26621540.22672571272598
3.3169-3.79660.25491340.208626612795100
3.7966-4.78210.20891430.178926752818100
4.7821-40.50640.231410.21232655279699

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