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- PDB-6wmw: GFRAL receptor bound with two antibody Fabs (3P10, 25M22) -

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Basic information

Entry
Database: PDB / ID: 6wmw
TitleGFRAL receptor bound with two antibody Fabs (3P10, 25M22)
Components
  • FAB25M22 heavy chain fragment
  • FAB25M22 light chain
  • FAB3P10 heavy chain fragment
  • FAB3P10 light chain
  • GDNF family receptor alpha-like
KeywordsIMMUNE SYSTEM / RECEPTOR / SIGNALING / ANTIBODES
Function / homology
Function and homology information


response to metformin / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / GDF15-GFRAL signaling pathway / negative regulation of appetite / stress-activated protein kinase signaling cascade / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / hormone activity / receptor tyrosine kinase binding / nervous system development ...response to metformin / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / GDF15-GFRAL signaling pathway / negative regulation of appetite / stress-activated protein kinase signaling cascade / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / hormone activity / receptor tyrosine kinase binding / nervous system development / signaling receptor activity / actin cytoskeleton / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / external side of plasma membrane / focal adhesion / nucleoplasm / plasma membrane
Similarity search - Function
Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
GDNF family receptor alpha-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsWhite, A. / Lakshminarasimhan, D. / Olland, A. / Suto, R.K.
CitationJournal: Nat Med / Year: 2020
Title: Antibody-mediated inhibition of GDF15-GFRAL activity reverses cancer cachexia in mice.
Authors: Suriben, R. / Chen, M. / Higbee, J. / Oeffinger, J. / Ventura, R. / Li, B. / Mondal, K. / Gao, Z. / Ayupova, D. / Taskar, P. / Li, D. / Starck, S.R. / Chen, H.H. / McEntee, M. / Katewa, S.D. ...Authors: Suriben, R. / Chen, M. / Higbee, J. / Oeffinger, J. / Ventura, R. / Li, B. / Mondal, K. / Gao, Z. / Ayupova, D. / Taskar, P. / Li, D. / Starck, S.R. / Chen, H.H. / McEntee, M. / Katewa, S.D. / Phung, V. / Wang, M. / Kekatpure, A. / Lakshminarasimhan, D. / White, A. / Olland, A. / Haldankar, R. / Solloway, M.J. / Hsu, J.Y. / Wang, Y. / Tang, J. / Lindhout, D.A. / Allan, B.B.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GDNF family receptor alpha-like
H: FAB3P10 heavy chain fragment
L: FAB3P10 light chain
M: FAB25M22 heavy chain fragment
N: FAB25M22 light chain


Theoretical massNumber of molelcules
Total (without water)127,0575
Polymers127,0575
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.498, 116.052, 227.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GDNF family receptor alpha-like


Mass: 27665.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRAL, C6orf144, UNQ9356/PRO34128 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6UXV0
#2: Antibody FAB3P10 heavy chain fragment


Mass: 24098.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody FAB3P10 light chain


Mass: 23745.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody FAB25M22 heavy chain fragment


Mass: 24894.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody FAB25M22 light chain


Mass: 26652.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M IMIDAZOLE Ph 7.0 AND 12% (w/w) peg 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 31586 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 0.996 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.91-3.015.90.78730180.7180.3490.864198.8
3.01-3.136.20.55531060.8430.240.606198.9
3.13-3.286.30.36131090.920.1550.3940.98799.2
3.28-3.456.40.24530980.9670.1040.2671.00599.8
3.45-3.676.60.15931220.9840.0660.1721.00299.8
3.67-3.956.90.1231410.9920.0490.131.003100
3.95-4.3570.08931820.9960.0360.0961.007100
4.35-4.977.10.06631610.9970.0270.0710.993100
4.97-6.276.90.07732330.9960.0310.0830.999100
6.27-506.50.04434160.9990.0180.0470.96799.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vz4

5vz4


Resolution: 2.91→47.7 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.882 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 1591 5 %RANDOM
Rwork0.2216 ---
obs0.2251 29927 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.9 Å2 / Biso mean: 75.054 Å2 / Biso min: 26.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0 Å2
2---0.98 Å20 Å2
3---1.24 Å2
Refinement stepCycle: final / Resolution: 2.91→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8097 0 0 0 8097
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148301
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177287
X-RAY DIFFRACTIONr_angle_refined_deg1.241.65511286
X-RAY DIFFRACTIONr_angle_other_deg0.7891.63917134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54351053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01423.425362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.764151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6681530
X-RAY DIFFRACTIONr_chiral_restr0.0550.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021543
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 117 -
Rwork0.332 2037 -
all-2154 -
obs--95.23 %

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