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- PDB-5d22: Structure of ovine granulocyte-macrophage colony-stimulating factor -

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Basic information

Entry
Database: PDB / ID: 5d22
TitleStructure of ovine granulocyte-macrophage colony-stimulating factor
ComponentsGranulocyte-macrophage colony-stimulating factor
KeywordsCYTOKINE / Signaling Protein / recombinant proteins / cytokine immunology
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor binding / neutrophil differentiation / positive regulation of interleukin-23 production / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / myeloid dendritic cell differentiation / positive regulation of leukocyte proliferation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of macrophage derived foam cell differentiation / positive regulation of podosome assembly ...granulocyte macrophage colony-stimulating factor receptor binding / neutrophil differentiation / positive regulation of interleukin-23 production / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / myeloid dendritic cell differentiation / positive regulation of leukocyte proliferation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of macrophage derived foam cell differentiation / positive regulation of podosome assembly / monocyte differentiation / macrophage differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor signaling pathway via JAK-STAT / embryonic placenta development / cytokine activity / growth factor activity / cell population proliferation / immune response / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / extracellular space
Similarity search - Function
Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsFelix, J. / Savvides, S.N.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
Authors: Jan Felix / Eaazhisai Kandiah / Steven De Munck / Yehudi Bloch / Gydo C P van Zundert / Kris Pauwels / Ann Dansercoer / Katka Novanska / Randy J Read / Alexandre M J J Bonvin / Bjorn ...Authors: Jan Felix / Eaazhisai Kandiah / Steven De Munck / Yehudi Bloch / Gydo C P van Zundert / Kris Pauwels / Ann Dansercoer / Katka Novanska / Randy J Read / Alexandre M J J Bonvin / Bjorn Vergauwen / Kenneth Verstraete / Irina Gutsche / Savvas N Savvides /
Abstract: Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen ...Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive. Here we reveal that GIF employs a dimeric binding platform that sequesters two copies of its target cytokines with high affinity and slow dissociation kinetics to yield distinct complexes featuring mutually exclusive interaction footprints. We illustrate how GIF serves as a competitive decoy receptor by leveraging binding hotspots underlying the cognate receptor interactions of GM-CSF and IL-2, without sharing any structural similarity with the cytokine receptors. Our findings contribute to the tracing of novel molecular mimicry mechanisms employed by pathogenic viruses.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granulocyte-macrophage colony-stimulating factor
B: Granulocyte-macrophage colony-stimulating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0335
Polymers28,8532
Non-polymers1803
Water2,180121
1
A: Granulocyte-macrophage colony-stimulating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5473
Polymers14,4261
Non-polymers1212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Granulocyte-macrophage colony-stimulating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4852
Polymers14,4261
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.100, 77.020, 47.450
Angle α, β, γ (deg.)90.00, 111.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Granulocyte-macrophage colony-stimulating factor / GM-CSF / Colony-stimulating factor / CSF


Mass: 14426.386 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: CSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P28773
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate 0.1 M TRIS hydrochloride pH 8.5 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.239 Å / Relative weight: 1
ReflectionResolution: 1.99→38.51 Å / Num. all: 18842 / Num. obs: 18252 / % possible obs: 96.9 % / Redundancy: 3.28 % / Rsym value: 0.129 / Net I/σ(I): 8.17
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3.14 % / Mean I/σ(I) obs: 2.12 / Rsym value: 0.732 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GMF

2gmf


Resolution: 1.994→38.51 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 900 5 %
Rwork0.1881 --
obs0.19 18017 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.994→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 12 121 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091981
X-RAY DIFFRACTIONf_angle_d1.0682685
X-RAY DIFFRACTIONf_dihedral_angle_d12.777734
X-RAY DIFFRACTIONf_chiral_restr0.049310
X-RAY DIFFRACTIONf_plane_restr0.006343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9943-2.11920.32771380.28812667X-RAY DIFFRACTION91
2.1192-2.28290.28851520.24732853X-RAY DIFFRACTION96
2.2829-2.51260.24971500.2162829X-RAY DIFFRACTION95
2.5126-2.8760.2451500.19612889X-RAY DIFFRACTION98
2.876-3.62310.24261540.17692933X-RAY DIFFRACTION98
3.6231-38.51720.17511560.15252946X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 3.6389 Å / Origin y: -18.0912 Å / Origin z: -9.3264 Å
111213212223313233
T0.2436 Å2-0.0429 Å20.0148 Å2-0.236 Å2-0.0164 Å2--0.264 Å2
L0.7692 °2-0.4638 °20.4686 °2-0.6854 °2-0.2923 °2--1.1407 °2
S-0.0122 Å °-0.0032 Å °-0.02 Å °-0.0281 Å °0.0123 Å °-0.0039 Å °0.0081 Å °-0.0134 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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