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- PDB-1btg: CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION... -

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Basic information

Entry
Database: PDB / ID: 1btg
TitleCRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND
ComponentsBETA NERVE GROWTH FACTOR
KeywordsGROWTH FACTOR / NERVE
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: 2.5 Å
AuthorsHolland, D.R. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Nerve growth factor in different crystal forms displays structural flexibility and reveals zinc binding sites.
Authors: Holland, D.R. / Cousens, L.S. / Meng, W. / Matthews, B.W.
History
DepositionAug 29, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 22, 2020Group: Data collection / Other / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_source / pdbx_database_status / software
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_detector.details / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.target / _diffrn_source.type / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf

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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
C: BETA NERVE GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3426
Polymers37,1463
Non-polymers1963
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BETA NERVE GROWTH FACTOR

A: BETA NERVE GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)24,7642
Polymers24,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area2390 Å2
ΔGint-17 kcal/mol
Surface area12270 Å2
MethodPISA, PQS
3
B: BETA NERVE GROWTH FACTOR
C: BETA NERVE GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9605
Polymers24,7642
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-103 kcal/mol
Surface area12080 Å2
MethodPISA
4
B: BETA NERVE GROWTH FACTOR
C: BETA NERVE GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9605
Polymers24,7642
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation3_546x+1/2,y-1/2,z+11
MethodPQS
Unit cell
Length a, b, c (Å)109.800, 93.900, 58.900
Angle α, β, γ (deg.)90.00, 123.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETA NERVE GROWTH FACTOR / BNGF


Mass: 12382.035 Da / Num. of mol.: 3
Mutation: BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED)
Source method: isolated from a genetically manipulated source
Details: ZN IONS BOUND / Source: (gene. exp.) Mus musculus (house mouse) / Organ: SALIVARY GLANDS / References: UniProt: P01139
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
pH: 6.1 / Method: vapor diffusion / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
218-20 %PEG80001reservoir
3100 mMPIPES1reservoir
4100 mMzinc acetate1reservoir

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 298 K
Diffraction sourceSource: rotating-anode X-ray tube / Type: RIGAKU RU200 / Wavelength: 1.54 / Target: Cu
DetectorType: AREA DETECTOR / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: Xuong-Hamlin
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 15194 / % possible obs: 89 % / Num. measured all: 44269 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
HOWARDET AL.data collection
TNTrefinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
Xengen (HOWARD, NIELSEN, XUONG)data scaling
RefinementResolution: 2.5→20 Å / σ(F): 2
Details: ALTHOUGH THE N- AND C-TERMINI OF THE A, B, AND C MOLECULES ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS, THEY ARE SEEN IN OMIT MAPS.
RfactorNum. reflection
obs0.179 44269
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 3 54 2565
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0140.02
X-RAY DIFFRACTIONt_angle_deg2.42.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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