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- PDB-5d72: Crystal structure of MOR04252, a neutralizing anti-human GM-CSF a... -

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Basic information

Entry
Database: PDB / ID: 5d72
TitleCrystal structure of MOR04252, 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 / histamine secretion / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway ...granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production / regulation of circadian sleep/wake cycle, sleep / dendritic cell differentiation / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / response to fluid shear stress / myeloid dendritic cell differentiation / positive regulation of leukocyte proliferation / myeloid cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cell surface receptor signaling pathway via STAT / positive regulation of macrophage derived foam cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / Interleukin-10 signaling / monocyte differentiation / macrophage differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / embryonic placenta development / cytokine activity / growth factor activity / cellular response to lipopolysaccharide / RAF/MAP kinase cascade / cell population proliferation / immune response / positive regulation of cell migration / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / 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: 2.6 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
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
B: Granulocyte-macrophage colony-stimulating factor
H: Immunglobulin G1 Fab fragment, heavy chain
L: Immunglobulin G1 Fab fragment, light chain
M: Immunglobulin G1 Fab fragment, heavy chain
N: Immunglobulin G1 Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4958
Polymers127,2836
Non-polymers2122
Water57632
1
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)63,7474
Polymers63,6413
Non-polymers1061
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-32 kcal/mol
Surface area24880 Å2
MethodPISA
2
B: Granulocyte-macrophage colony-stimulating factor
M: Immunglobulin G1 Fab fragment, heavy chain
N: Immunglobulin G1 Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7474
Polymers63,6413
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-31 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.822, 97.853, 192.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15953.349 Da / Num. of mol.: 2
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: 25458.283 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.62 Å3/Da / Density % sol: 53 %
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, 30 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: 2.6→96.22 Å / Num. obs: 42619 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.74
Reflection shellResolution: 2.6→2.77 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.715 / % possible all: 98

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→96.22 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 28.435 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26636 897 2.1 %RANDOM
Rwork0.23155 ---
obs0.23231 40852 97.96 %-
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: 67.877 Å2
Baniso -1Baniso -2Baniso -3
1--5.43 Å20 Å20 Å2
2--9.97 Å20 Å2
3----4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→96.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8096 0 14 32 8142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227964
X-RAY DIFFRACTIONr_bond_other_d0.0020.026925
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.94910912
X-RAY DIFFRACTIONr_angle_other_deg0.884316018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05151058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9924.109275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.504151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5051524
X-RAY DIFFRACTIONr_chiral_restr0.0660.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021569
X-RAY DIFFRACTIONr_nbd_refined0.1510.21147
X-RAY DIFFRACTIONr_nbd_other0.1350.26115
X-RAY DIFFRACTIONr_nbtor_refined0.1540.23794
X-RAY DIFFRACTIONr_nbtor_other0.0720.24412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1030.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.14126737
X-RAY DIFFRACTIONr_mcbond_other0.19522159
X-RAY DIFFRACTIONr_mcangle_it1.51238499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17443202
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.04862412
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 54 -
Rwork0.421 2983 -
obs--97.46 %
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)
15.0133-0.3672-2.24261.31611.75235.8922-0.0442-0.4332-0.08660.28440.01890.06260.20380.13910.0253-0.27250.0202-0.0464-0.3670.0538-0.321523.01912.03258.791
27.8039-1.25822.06472.2983-0.70164.51520.2116-0.231-0.23520.04360.00580.21110.1753-0.0964-0.2175-0.39-0.07310.0259-0.4101-0.0273-0.381413.558.90834.097
37.2089-0.12282.35231.5863-1.8124.14910.16871.2874-0.1752-0.1444-0.16180.26650.38150.7619-0.007-0.29170.0783-0.0488-0.00250.0459-0.414112.41817.255-2.844
42.69270.27970.74970.3614-0.01814.4343-0.00830.18370.0057-0.0849-0.0505-0.1590.20260.40080.0589-0.39950.03730.0108-0.44890.0171-0.351235.96211.77129.98
53.52530.20251.65824.198-1.16063.34380.13760.55310.631-0.2333-0.18140.0217-0.19530.20220.0437-0.40020.02010.0985-0.02290.0953-0.288925.8824.3144.657
63.56340.5916-0.14862.85390.26023.81690.0279-0.34940.35120.5005-0.06580.0273-0.31380.02520.0379-0.23680.0291-0.0498-0.3774-0.0062-0.282511.246-18.41860.579
73.06690.1171-0.18951.59720.65363.9497-0.01630.26960.1343-0.07370.0109-0.14980.03110.48090.0055-0.41960.03810.0185-0.39870.0534-0.368822.199-27.79232.193
85.0622-1.16231.61863.7886-1.3724.6570.1880.13310.3077-0.2278-0.11620.3528-0.11430.2202-0.0719-0.3704-0.00950.06830.0152-0.0737-0.349211.362-23.4483.779
94.32510.20471.13091.26220.3192.61520.0871-0.13710.09320.1654-0.08970.1447-0.0203-0.19650.0027-0.34140.00170.0497-0.4286-0.0177-0.3620.227-27.08437.503
106.85510.82980.26721.8789-0.69944.5117-0.01230.335-0.6944-0.21430.0710.11220.16250.4525-0.0586-0.2699-0.0236-0.0534-0.1318-0.0291-0.2972-2.194-31.8930.099
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 124
2X-RAY DIFFRACTION2L1 - 105
3X-RAY DIFFRACTION3L108 - 208
4X-RAY DIFFRACTION4H1 - 105
5X-RAY DIFFRACTION5H108 - 214
6X-RAY DIFFRACTION6B8 - 124
7X-RAY DIFFRACTION7M1 - 105
8X-RAY DIFFRACTION8M108 - 213
9X-RAY DIFFRACTION9N1 - 105
10X-RAY DIFFRACTION10N108 - 208

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