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- PDB-1agq: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT -

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Basic information

Entry
Database: PDB / ID: 1agq
TitleGLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT
ComponentsGLIAL CELL-DERIVED NEUROTROPHIC FACTOR
KeywordsGROWTH FACTOR / NEUROTROPHIC FACTOR / CYSTINE KNOT
Function / homology
Function and homology information


regulation of ureteric bud formation / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / ureteric bud formation / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / glial cell-derived neurotrophic factor receptor binding / RET signaling ...regulation of ureteric bud formation / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / ureteric bud formation / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / glial cell-derived neurotrophic factor receptor binding / RET signaling / postsynaptic membrane organization / glial cell-derived neurotrophic factor receptor signaling pathway / regulation of morphogenesis of a branching structure / organ induction / peristalsis / regulation of dopamine uptake involved in synaptic transmission / neural crest cell migration involved in autonomic nervous system development / negative regulation of glial cell apoptotic process / sympathetic nervous system development / enteric nervous system development / peripheral nervous system development / metanephros development / positive regulation of branching involved in ureteric bud morphogenesis / neural crest cell migration / commissural neuron axon guidance / ureteric bud development / branching involved in ureteric bud morphogenesis / RAF/MAP kinase cascade / mRNA stabilization / negative regulation of interleukin-1 beta production / midbrain development / cellular response to dexamethasone stimulus / retina development in camera-type eye / positive regulation of interleukin-10 production / embryonic organ development / negative regulation of tumor necrosis factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / positive regulation of cell differentiation / male gonad development / receptor tyrosine kinase binding / neuron projection development / neuron differentiation / nervous system development / regulation of gene expression / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor complex / receptor ligand activity / positive regulation of cell population proliferation / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / : / extracellular region
Similarity search - Function
Glial cell line-derived neurotrophic factor / : / Glial cell line-derived neurotrophic factor family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Glial cell line-derived neurotrophic factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsEigenbrot, C. / Gerber, N.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: X-ray structure of glial cell-derived neurotrophic factor at 1.9 A resolution and implications for receptor binding.
Authors: Eigenbrot, C. / Gerber, N.
#1: Journal: Annu.Rev.Biophys.Biomol.Struct. / Year: 1995
Title: The Cystine-Knot Growth-Factor Superfamily
Authors: Sun, P.D. / Davies, D.R.
#2: Journal: Science / Year: 1993
Title: A Glial Cell Line-Derived Neurotrophic Factor for Midbrain Dopaminergic Neurons
Authors: Lin, L.F. / Doherty, D.H. / Lile, J.D. / Bektesh, S. / Collins, F.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR
B: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR
C: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR
D: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR


Theoretical massNumber of molelcules
Total (without water)60,3614
Polymers60,3614
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.850, 67.550, 71.400
Angle α, β, γ (deg.)90.00, 115.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.131915, 0.517078, -0.845712), (0.528292, -0.758579, -0.3814), (-0.838753, -0.39647, -0.373237)24.8478, 38.8802, 58.1358
2given(0.559989, 0.039033, 0.82758), (0.087061, -0.996132, -0.011928), (0.823913, 0.07873, -0.561221)3.8962, 15.991, 2.5719
3given(-0.75666, -0.611477, 0.231434), (-0.215165, 0.567151, 0.795012), (-0.617389, 0.551757, -0.560709)38.832, 29.2662, 44.4868

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Components

#1: Protein
GLIAL CELL-DERIVED NEUROTROPHIC FACTOR / GDNF


Mass: 15090.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: GLIA / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q07731
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.4 Å3/Da / Density % sol: 42 %
Crystal growpH: 7 / Details: 20% PEG 6000, 0.8 M LICL, PH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.1 mg/mlprotein1drop
230 mMHEPES1drop
30.012 %(w/v)sodium azide1drop
40.06 mMbenzamidine1drop
58 %(w/v)PEG60001reservoir
60.32 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Feb 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 46219 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.054 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.228 / % possible all: 98.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
XSIGHTmodel building
X-PLOR3.851refinement
XSIGHTphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED. THERE ARE 139 ATOMS ASSIGNED ZERO OCCUPANCY. SOME OF THESE WERE USED WITH UNIT OCCUPANCY AT SOME STAGE OF REFINEMENT, BUT ...Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED. THERE ARE 139 ATOMS ASSIGNED ZERO OCCUPANCY. SOME OF THESE WERE USED WITH UNIT OCCUPANCY AT SOME STAGE OF REFINEMENT, BUT ARE NOW ASSIGNED ZERO OCCUPANCY. THE SEGMENT C 116 - C 120 IS POORLY MODELED USING A SINGLE MAIN CHAIN CONFORMATION. THERE IS RESIDUAL ELECTRON DENSITY SUGGESTING ADDITIONAL CONFORMATION(S), BUT NO ATTEMPT TO MODEL THEM HAS BEEN MADE. ALL RESIDUE NUMBERS IN THIS ENTRY ARE GREATER (BY ONE) THAN THOSE USED IN THE JOURNAL ARTICLE DESCRIBING THIS WORK (JRNL RECORD).
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4402 10.2 %RANDOM
Rwork0.203 ---
obs0.203 43042 93.9 %-
Displacement parametersBiso mean: 33.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 0 285 3226
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.79
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.054
X-RAY DIFFRACTIONx_mcangle_it4.985
X-RAY DIFFRACTIONx_scbond_it7.178
X-RAY DIFFRACTIONx_scangle_it9.19
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.269 347 9.6 %
Rwork0.189 3258 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.79

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