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- PDB-5d71: Crystal structure of MOR04302, a neutralizing anti-human GM-CSF a... -

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Basic information

Entry
Database: PDB / ID: 5d71
TitleCrystal structure of MOR04302, a neutralizing anti-human GM-CSF antibody Fab fragment in complex with human GM-CSF
Components
  • (Immunglobulin G1 Fab fragment, ...) x 2
  • Granulocyte-macrophage colony-stimulating factor
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 / histamine secretion / neutrophil differentiation / response to silicon dioxide / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / response to fluid shear stress / positive regulation of macrophage derived foam cell differentiation ...granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / neutrophil differentiation / response to silicon dioxide / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / response to fluid shear stress / positive regulation of macrophage derived foam cell differentiation / myeloid dendritic cell differentiation / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / myeloid cell differentiation / positive regulation of leukocyte proliferation / 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 / cell surface receptor signaling pathway via JAK-STAT / monocyte differentiation / 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
DI(HYDROXYETHYL)ETHER / Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)64,1596
Polymers63,8603
Non-polymers2983
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-59 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.680, 158.680, 158.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 16309.723 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

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Antibody , 2 types, 2 molecules HL

#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: 22229.715 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)

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Non-polymers , 3 types, 201 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 100 mM sodium acetate, pH 4.0-4.3, 39-42 % (w/v) PEG 400, 35 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 2.25→112.2 Å / Num. obs: 31568 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 24.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.33
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 24.3 % / Rmerge(I) obs: 0.66 / % possible all: 99.3

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Processing

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

2gmf


Resolution: 2.25→112.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.026 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21898 1393 4.4 %RANDOM
Rwork0.17957 ---
obs0.18132 30163 99.96 %-
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: 51.358 Å2
Refinement stepCycle: LAST / Resolution: 2.25→112.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 17 198 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223962
X-RAY DIFFRACTIONr_bond_other_d0.0020.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.955416
X-RAY DIFFRACTIONr_angle_other_deg0.93437997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29424.161137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8151512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024461
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02776
X-RAY DIFFRACTIONr_nbd_refined0.1730.2549
X-RAY DIFFRACTIONr_nbd_other0.1570.22967
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21845
X-RAY DIFFRACTIONr_nbtor_other0.0760.22132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.06223320
X-RAY DIFFRACTIONr_mcbond_other0.49221066
X-RAY DIFFRACTIONr_mcangle_it2.68934196
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.91341622
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.00761220
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: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 95 -
Rwork0.233 2216 -
obs--99.74 %
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)
12.4699-1.0334-0.36562.0584-0.44256.5508-0.012-0.2952-0.31290.41970.02070.0893-0.0250.059-0.00880.02160.0965-0.0204-0.0425-0.00630.055591.187108.97734.661
20.8378-1.64380.18296.07671.85222.3853-0.1806-0.23520.03810.17410.1760.12050.0853-0.16850.0045-0.19060.03360.0159-0.06610.0133-0.12599.16992.13812.929
32.91130.7815-1.10951.9932-1.58996.0907-0.10680.1265-0.0097-0.12040.0877-0.04240.2459-0.1660.019-0.1603-0.0597-0.034-0.1064-0.0094-0.1575112.60287.005-14.466
41.5295-0.852-0.66573.00860.35362.7998-0.14120.05790.0237-0.30160.09560.2669-0.1341-0.17490.0457-0.11660.0431-0.0864-0.1059-0.0148-0.049187.512108.6172.606
54.8494-2.48410.39654.4550.1733.83180.22270.3366-0.7012-0.1139-0.0896-0.0130.3240.3074-0.1331-0.1127-0.0674-0.0863-0.0679-0.0291-0.018599.97685.497-24.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 122
2X-RAY DIFFRACTION2L1 - 105
3X-RAY DIFFRACTION3L108 - 209
4X-RAY DIFFRACTION4H1 - 105
5X-RAY DIFFRACTION5H108 - 213

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