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- PDB-5d70: Crystal structure of MOR03929, a neutralizing anti-human GM-CSF a... -

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Basic information

Entry
Database: PDB / ID: 5d70
TitleCrystal structure of MOR03929, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF
Components
  • Granulocyte-macrophage colony-stimulating factor
  • Immunglobulin G1 Fab fragment, heavy chain
  • Immunglobulin G1 Fab fragment, light chain
KeywordsIMMUNE SYSTEM / GM-CSF / affinity maturation / phage display / cytokine / antibody / PROTEROS BIOSTRUCTURES GMBH
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 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / 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 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsEylenstein, R. / Weinfurtner, D. / Steidl, S. / Boettcher, J. / Augustin, M.
CitationJournal: Mabs / Year: 2016
Title: Molecular basis of in vitro affinity maturation and functional evolution of a neutralizing anti-human GM-CSF antibody.
Authors: Eylenstein, R. / Weinfurtner, D. / Hartle, S. / Strohner, R. / Bottcher, J. / Augustin, M. / Ostendorp, R. / Steidl, S.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Granulocyte-macrophage colony-stimulating factor
H: Immunglobulin G1 Fab fragment, heavy chain
L: Immunglobulin G1 Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1394
Polymers62,0433
Non-polymers961
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-47 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.235, 158.235, 158.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: 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
#2: Antibody Immunglobulin G1 Fab fragment, heavy chain


Mass: 25321.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Immunglobulin G1 Fab fragment, light chain


Mass: 22229.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 100 mM Tris, pH 8.75, 200 mM LiSO4, 25-28 % (w/v) PEG 3350, 28mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0015 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.06→111.89 Å / Num. obs: 40747 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 21.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 27.58
Reflection shellResolution: 2.06→2.24 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.734 / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C7X and 2GMF

5c7x

2gmf


Resolution: 2.06→111.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.341 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22179 1777 4.4 %RANDOM
Rwork0.18998 ---
obs0.19135 38872 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.433 Å2
Refinement stepCycle: LAST / Resolution: 2.06→111.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 5 330 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224020
X-RAY DIFFRACTIONr_bond_other_d0.0020.023494
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9525498
X-RAY DIFFRACTIONr_angle_other_deg0.91738147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21524.631149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94115595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2661512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
X-RAY DIFFRACTIONr_nbd_refined0.1690.2556
X-RAY DIFFRACTIONr_nbd_other0.1520.23136
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21864
X-RAY DIFFRACTIONr_nbtor_other0.0750.22117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.74123346
X-RAY DIFFRACTIONr_mcbond_other0.3921066
X-RAY DIFFRACTIONr_mcangle_it2.19734224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.26441678
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.23461272
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 148 -
Rwork0.23 2877 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0282-0.94410.03391.3526-0.60085.8945-0.0367-0.2969-0.18850.28960.012-0.0295-0.0910.06930.0246-0.04010.0762-0.0062-0.06390.0024-0.040591.177108.77734.821
20.534-0.5695-0.63341.24921.14732.5402-0.10730.0671-0.0126-0.1850.05240.1715-0.1236-0.14380.0548-0.12810.0204-0.0418-0.11480.0032-0.094687.723107.5290.299
36.8895-1.90281.27355.8842-0.04823.16650.38630.4716-1.1561-0.2704-0.09060.05140.44480.2076-0.2958-0.0913-0.0481-0.0826-0.064-0.06830.0282100.56982.736-25.121
40.6558-0.77630.21694.73611.52031.8763-0.1266-0.1662-0.08340.14460.15070.15570.1237-0.1765-0.024-0.16770.02220.0382-0.10040.0429-0.14799.29390.65511.987
53.38920.9262-1.02882.0398-1.81867.1292-0.09280.154-0.0505-0.15940.0768-0.03410.2411-0.13670.016-0.1633-0.0454-0.0016-0.112-0.0369-0.1748112.47987.327-15.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 122
2X-RAY DIFFRACTION2H1 - 122
3X-RAY DIFFRACTION3H123 - 214
4X-RAY DIFFRACTION4L1 - 112
5X-RAY DIFFRACTION5L113 - 209

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