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- PDB-2gyr: Crystal structure of human artemin -

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Basic information

Entry
Database: PDB / ID: 2gyr
TitleCrystal structure of human artemin
ComponentsNeurotrophic factor artemin, isoform 3
KeywordsHORMONE/GROWTH FACTOR / neurotrophic factor / cystein-knot / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / RET signaling / neuroblast proliferation / axon guidance ...glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / RET signaling / neuroblast proliferation / axon guidance / growth factor activity / receptor tyrosine kinase binding / RAF/MAP kinase cascade / signaling receptor binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
Glial cell line-derived neurotrophic factor family / Transforming growth factor-beta (TGF-beta) 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsWang, X.Q.
CitationJournal: Structure / Year: 2006
Title: Structure of Artemin Complexed with Its Receptor GFRalpha3: Convergent Recognition of Glial Cell Line-Derived Neurotrophic Factors.
Authors: Wang, X. / Baloh, R.H. / Milbrandt, J. / Garcia, K.C.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotrophic factor artemin, isoform 3
B: Neurotrophic factor artemin, isoform 3
C: Neurotrophic factor artemin, isoform 3
D: Neurotrophic factor artemin, isoform 3
E: Neurotrophic factor artemin, isoform 3
F: Neurotrophic factor artemin, isoform 3


Theoretical massNumber of molelcules
Total (without water)69,4466
Polymers69,4466
Non-polymers00
Water00
1
A: Neurotrophic factor artemin, isoform 3
B: Neurotrophic factor artemin, isoform 3


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers23,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19 kcal/mol
Surface area10370 Å2
MethodPISA
2
C: Neurotrophic factor artemin, isoform 3
D: Neurotrophic factor artemin, isoform 3


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers23,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-19 kcal/mol
Surface area10270 Å2
MethodPISA
3
E: Neurotrophic factor artemin, isoform 3
F: Neurotrophic factor artemin, isoform 3


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers23,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-19 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 94.200, 219.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Neurotrophic factor artemin, isoform 3


Mass: 11574.299 Da / Num. of mol.: 6 / Fragment: N-terminal truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARTN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5T4W7
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: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 12-16% PEG3350, 0.1 M Hepes (pH 7.5), 0.1 M magnesium chloride, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2005
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 33877 / Num. obs: 33810 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
SHELXDphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.353 3169 random
Rwork0.308 --
all0.32 33877 -
obs0.314 31882 -
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 0 0 4410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.09

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