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- PDB-1bet: NEW PROTEIN FOLD REVEALED BY A 2.3 ANGSTROM RESOLUTION CRYSTAL ST... -

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Basic information

Entry
Database: PDB / ID: 1bet
TitleNEW PROTEIN FOLD REVEALED BY A 2.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NERVE GROWTH FACTOR
ComponentsBETA-NERVE GROWTH FACTOR
KeywordsGROWTH FACTOR
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 / positive regulation of neuron maturation / metalloendopeptidase inhibitor activity / 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 / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / positive regulation of axon extension / positive regulation of DNA binding / positive regulation of protein autophosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / sensory perception of pain / positive regulation of neuron differentiation / adult locomotory behavior / neuron projection morphogenesis / positive regulation of protein ubiquitination / endosome lumen / cell surface receptor protein tyrosine kinase signaling pathway / 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
Beta-nerve growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMcdonald, N.Q. / Lapatto, R. / Murray-Rust, J. / Gunning, J. / Wlodawer, A. / Blundell, T.L.
CitationJournal: Nature / Year: 1991
Title: New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor.
Authors: McDonald, N.Q. / Lapatto, R. / Murray-Rust, J. / Gunning, J. / Wlodawer, A. / Blundell, T.L.
History
DepositionApr 8, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-NERVE GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)11,9931
Polymers11,9931
Non-polymers00
Water57632
1
A: BETA-NERVE GROWTH FACTOR

A: BETA-NERVE GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)23,9852
Polymers23,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area11610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.480, 56.480, 182.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein BETA-NERVE GROWTH FACTOR


Mass: 11992.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01139
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal grow
*PLUS
pH: 6.8 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMphosphate11
2MPD11

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 7522 / % possible obs: 90.3 % / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
RESTRAINrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.22 / Rfactor obs: 0.22
Details: THERE IS VERY POOR ELECTRON DENSITY FOR THE ASN 43 - SER 47 LOOP. THERE IS NO FITTABLE DENSITY FOR RESIDUES 1 - 9 OR FOR THE C-TERMINUS.
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 32 872
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.04

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