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- PDB-5mr4: Ligand-receptor complex. -

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Basic information

Entry
Database: PDB / ID: 5mr4
TitleLigand-receptor complex.
Components
  • GDNF family receptor alpha-2GFRα
  • Neurturin
KeywordsSIGNALING PROTEIN / Complex / Signalling / Receptor
Function / homology
Function and homology information


glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway ...glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / receptor tyrosine kinase binding / neuron projection development / MAPK cascade / nervous system development / RAF/MAP kinase cascade / receptor complex / external side of plasma membrane / axon / signaling receptor binding / extracellular region / plasma membrane
Similarity search - Function
Glial cell line-derived neurotrophic factor receptor alpha 2 / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...Glial cell line-derived neurotrophic factor receptor alpha 2 / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / GDNF family receptor alpha-2 / Neurturin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSandmark, J. / Oster, L. / Aagaard, A. / Roth, R.G. / Dahl, G.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure and biophysical characterization of the human full-length neurturin-GFRa2 complex: A role for heparan sulfate in signaling.
Authors: Sandmark, J. / Dahl, G. / Oster, L. / Xu, B. / Johansson, P. / Akerud, T. / Aagaard, A. / Davidsson, P. / Bigalke, J.M. / Winzell, M.S. / Rainey, G.J. / Roth, R.G.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurturin
B: Neurturin
C: GDNF family receptor alpha-2
D: GDNF family receptor alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5228
Polymers125,2784
Non-polymers2444
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-2 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.810, 125.811, 82.722
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neurturin /


Mass: 11706.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRTN / Production host: Escherichia coli (E. coli) / References: UniProt: Q99748
#2: Protein GDNF family receptor alpha-2 / GFRα / GFR-alpha-2 / GDNF receptor beta / GDNFR-beta / Neurturin receptor alpha / NTNR-alpha / RET ligand ...GFR-alpha-2 / GDNF receptor beta / GDNFR-beta / Neurturin receptor alpha / NTNR-alpha / RET ligand 2 / TGF-beta-related neurotrophic factor receptor 2


Mass: 50932.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRA2, GDNFRB, RETL2, TRNR2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O00451
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 8% Tacsimate, 8% PEG MME 5000 and 0.1 M HEPES pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.985 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 2.4→55.8 Å / Num. obs: 60705 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MR5, 5MR9

5mr5

5mr9


Resolution: 2.4→49.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.537 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22002 3073 5.1 %RANDOM
Rwork0.19503 ---
obs0.19633 57605 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0.01 Å2
2--0.02 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 0 16 353 6448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196229
X-RAY DIFFRACTIONr_bond_other_d0.0060.025722
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9598398
X-RAY DIFFRACTIONr_angle_other_deg0.97313131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0515756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24522.26323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.139151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2451586
X-RAY DIFFRACTIONr_chiral_restr0.0810.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3565.0493054
X-RAY DIFFRACTIONr_mcbond_other3.3575.0493055
X-RAY DIFFRACTIONr_mcangle_it5.1717.5443800
X-RAY DIFFRACTIONr_mcangle_other5.1727.5463801
X-RAY DIFFRACTIONr_scbond_it4.6725.653175
X-RAY DIFFRACTIONr_scbond_other4.6525.6523169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3418.2264599
X-RAY DIFFRACTIONr_long_range_B_refined9.4339.1727085
X-RAY DIFFRACTIONr_long_range_B_other9.44339.1097041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 206 -
Rwork0.362 4265 -
obs--99.6 %

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