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- PDB-6bfs: The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies -

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Basic information

Entry
Database: PDB / ID: 6bfs
TitleThe mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies
Components
  • Fab Heavy Chain
  • Fab light Chain
  • Granulocyte-macrophage colony-stimulating factor
KeywordsIMMUNE SYSTEM / Cytokine-Fab complex / Pulmonary Alveolar Proteinosis / receptor assembly / autoantibodies
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor binding / neutrophil differentiation / histamine secretion / response to silicon dioxide / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / positive regulation of macrophage derived foam cell differentiation / response to fluid shear stress ...granulocyte macrophage colony-stimulating factor receptor binding / neutrophil differentiation / histamine secretion / response to silicon dioxide / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / positive regulation of macrophage derived foam cell differentiation / response to fluid shear stress / myeloid dendritic cell differentiation / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / positive regulation of leukocyte proliferation / myeloid cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / Interleukin-10 signaling / monocyte differentiation / cell surface receptor signaling pathway via JAK-STAT / macrophage differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / embryonic placenta development / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / RAF/MAP kinase cascade / cellular response to lipopolysaccharide / cell population proliferation / positive regulation of cell migration / immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / plasma membrane
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 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...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 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDhagat, U. / Hercus, T.R. / Broughton, S.E. / Nero, T.L. / Lopez, A.F. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: MAbs / Year: 2018
Title: The mechanism of GM-CSF inhibition by human GM-CSF auto-antibodies suggests novel therapeutic opportunities.
Authors: Dhagat, U. / Hercus, T.R. / Broughton, S.E. / Nero, T.L. / Cheung Tung Shing, K.S. / Barry, E.F. / Thomson, C.A. / Bryson, S. / Pai, E.F. / McClure, B.J. / Schrader, J.W. / Lopez, A.F. / Parker, M.W.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
Revision 1.6Nov 20, 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
L: Fab light Chain
H: Fab Heavy Chain
C: Granulocyte-macrophage colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)61,2133
Polymers61,2133
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-30 kcal/mol
Surface area23600 Å2
Unit cell
Length a, b, c (Å)70.454, 48.129, 77.602
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab light Chain


Mass: 23449.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Heavy Chain


Mass: 23270.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein Granulocyte-macrophage colony-stimulating factor / GM-CSF / Colony-stimulating factor / CSF / Molgramostin / Sargramostim


Mass: 14492.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2, GMCSF / Production host: Escherichia coli (E. coli) / References: UniProt: P04141
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop
Details: 0. 2 M Sodium Chloride, 20% PEG 8000, 0.1 M phosphate Citrate 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 34696 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.80.61325570.7720.3650.71499
8.95-39.553.40.0314210.9980.0190.03798.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å39.55 Å
Translation2 Å39.55 Å

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHASER2.5.7phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RJL

1rjl


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.216 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1671 4.8 %RANDOM
Rwork0.182 ---
obs0.185 33019 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.21 Å2 / Biso mean: 34.652 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å20.1 Å2
2--0.6 Å2-0 Å2
3---1.97 Å2
Refinement stepCycle: final / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 0 116 4244
Biso mean---34 -
Num. residues----535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024235
X-RAY DIFFRACTIONr_bond_other_d0.0020.023909
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.955762
X-RAY DIFFRACTIONr_angle_other_deg1.01139068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.725531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25324.727165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47115698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0051513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02927
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 144 -
Rwork0.271 2404 -
all-2548 -
obs--98.87 %

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