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- PDB-5vz4: Receptor-growth factor crystal structure at 2.20 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5vz4
TitleReceptor-growth factor crystal structure at 2.20 Angstrom resolution
Components
  • GDNF family receptor alpha-likeGFRα
  • Growth/differentiation factor 15
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / Receptor / growth factor / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / SMAD protein signal transduction / negative regulation of multicellular organism growth / stress-activated protein kinase signaling cascade / positive regulation of myoblast fusion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / transforming growth factor beta receptor signaling pathway ...negative regulation of growth hormone receptor signaling pathway / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / SMAD protein signal transduction / negative regulation of multicellular organism growth / stress-activated protein kinase signaling cascade / positive regulation of myoblast fusion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / receptor tyrosine kinase binding / actin cytoskeleton / cell-cell signaling / signaling receptor activity / nervous system development / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / focal adhesion / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine
Similarity search - Domain/homology
BROMIDE ION / GDNF family receptor alpha-like / Growth/differentiation factor 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLakshminarasimhan, D. / White, A. / Suto, R.K.
CitationJournal: Nature / Year: 2017
Title: Non-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15.
Authors: Hsu, J.Y. / Crawley, S. / Chen, M. / Ayupova, D.A. / Lindhout, D.A. / Higbee, J. / Kutach, A. / Joo, W. / Gao, Z. / Fu, D. / To, C. / Mondal, K. / Li, B. / Kekatpure, A. / Wang, M. / Laird, ...Authors: Hsu, J.Y. / Crawley, S. / Chen, M. / Ayupova, D.A. / Lindhout, D.A. / Higbee, J. / Kutach, A. / Joo, W. / Gao, Z. / Fu, D. / To, C. / Mondal, K. / Li, B. / Kekatpure, A. / Wang, M. / Laird, T. / Horner, G. / Chan, J. / McEntee, M. / Lopez, M. / Lakshminarasimhan, D. / White, A. / Wang, S.P. / Yao, J. / Yie, J. / Matern, H. / Solloway, M. / Haldankar, R. / Parsons, T. / Tang, J. / Shen, W.D. / Alice Chen, Y. / Tian, H. / Allan, B.B.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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: Growth/differentiation factor 15
B: GDNF family receptor alpha-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5079
Polymers39,9692
Non-polymers5387
Water2,594144
1
A: Growth/differentiation factor 15
B: GDNF family receptor alpha-like
hetero molecules

A: Growth/differentiation factor 15
B: GDNF family receptor alpha-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,01418
Polymers79,9384
Non-polymers1,07614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area7130 Å2
ΔGint-91 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.352, 88.768, 121.293
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Growth/differentiation factor 15 / GDF-15 / Macrophage inhibitory cytokine 1 / MIC-1 / NSAID-activated gene 1 protein / NAG-1 / NSAID- ...GDF-15 / Macrophage inhibitory cytokine 1 / MIC-1 / NSAID-activated gene 1 protein / NAG-1 / NSAID-regulated gene 1 protein / NRG-1 / Placental TGF-beta / Placental bone morphogenetic protein / Prostate differentiation factor


Mass: 12303.248 Da / Num. of mol.: 1 / Fragment: UNP residues 197-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF15, MIC1, PDF, PLAB, PTGFB / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q99988
#2: Protein GDNF family receptor alpha-like / GFRα


Mass: 27665.693 Da / Num. of mol.: 1 / Fragment: UNP residues 115-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRAL, C6orf144, UNQ9356/PRO34128 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6UXV0

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-Tris, pH 6.0, 1.5 M ammonium sulfate, 10% w/v ethylene glycol, 30-minute soak in 0.5 M sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→71.63 Å / Num. obs: 20379 / % possible obs: 97.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.039 / Rrim(I) all: 0.094 / Χ2: 1.033 / Net I/σ(I): 7.5 / Num. measured all: 118710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.90.57717830.8520.280.6441.04585.4
2.28-2.375.30.48618830.9060.2280.5391.0392.7
2.37-2.485.80.46520580.9410.2090.5111.02598.9
2.48-2.616.20.34320610.9740.1490.3751.03100
2.61-2.776.20.25720720.9830.1120.2811.006100
2.77-2.996.20.17920690.9880.0780.1951.041100
2.99-3.296.20.12120810.990.0540.1331.02699.9
3.29-3.766.10.07321010.9960.0330.081.01199.9
3.76-4.745.90.05521020.9970.0260.0611.05299.4
4.74-505.50.04521690.9970.0220.0511.06797.8

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VZ3 & 2GH0

5vz3

2gh0


Resolution: 2.2→71.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2704 / WRfactor Rwork: 0.1981 / FOM work R set: 0.7398 / SU B: 8.06 / SU ML: 0.189 / SU R Cruickshank DPI: 0.2206 / SU Rfree: 0.2055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1048 5.1 %RANDOM
Rwork0.1911 ---
obs0.1946 19330 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.24 Å2 / Biso mean: 56.934 Å2 / Biso min: 29.28 Å2
Baniso -1Baniso -2Baniso -3
1--4.22 Å20 Å20 Å2
2--6.09 Å20 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2.2→71.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 24 144 2463
Biso mean--72.71 57.55 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192372
X-RAY DIFFRACTIONr_bond_other_d0.0020.022198
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9483221
X-RAY DIFFRACTIONr_angle_other_deg1.05135071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6324.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06315398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4861515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02531
LS refinement shellResolution: 2.203→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 76 -
Rwork0.335 1187 -
all-1263 -
obs--82.66 %

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