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- PDB-5c7x: Crystal structure of MOR04357, a neutralizing anti-human GM-CSF a... -

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Basic information

Entry
Database: PDB / ID: 5c7x
TitleCrystal structure of MOR04357, 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 / 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 / positive regulation of leukocyte proliferation / response to fluid shear stress / myeloid dendritic cell differentiation / myeloid cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of macrophage derived foam cell differentiation / cell surface receptor signaling pathway via STAT / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / Interleukin-10 signaling / macrophage differentiation / monocyte differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / Chem-PG6 / TRIETHYLENE GLYCOL / Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsEylenstein, R. / Weinfurtner, D. / Steidl, S. / Boettcher, J. / Augustin, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry of Education and Research16EX1022K/L Germany
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
DepositionJun 25, 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
Revision 1.4Nov 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
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)125,24612
Polymers124,3616
Non-polymers8856
Water61334
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)62,8537
Polymers62,1803
Non-polymers6734
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-16 kcal/mol
Surface area24530 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)62,3935
Polymers62,1803
Non-polymers2122
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-29 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.602, 97.493, 192.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 14492.495 Da / Num. of mol.: 2 / Fragment: UNP residues 18-144
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, 4 molecules HMLN

#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: 22229.715 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)

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Non-polymers , 4 types, 40 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.35 %
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, 40 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: 2.95→96.26 Å / Num. obs: 29123 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.18 / Net I/av σ(I): 1.8 / Net I/σ(I): 6.8
Reflection shellResolution: 2.95→3.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.8 / % possible all: 95.5

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Processing

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

2gmf


Resolution: 2.95→96.26 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.87 / SU B: 20.364 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27613 593 2.2 %RANDOM
Rwork0.23353 ---
obs0.23449 26834 94.18 %-
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: 43.91 Å2
Baniso -1Baniso -2Baniso -3
1--5.15 Å20 Å20 Å2
2--10.2 Å20 Å2
3----5.05 Å2
Refinement stepCycle: LAST / Resolution: 2.95→96.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8091 0 59 34 8184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228019
X-RAY DIFFRACTIONr_bond_other_d0.0020.027008
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.95310959
X-RAY DIFFRACTIONr_angle_other_deg0.895316221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46651055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67524.235281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.774151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6021525
X-RAY DIFFRACTIONr_chiral_restr0.0670.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021567
X-RAY DIFFRACTIONr_nbd_refined0.1490.21351
X-RAY DIFFRACTIONr_nbd_other0.1370.26601
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23824
X-RAY DIFFRACTIONr_nbtor_other0.0730.24478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1040.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31526731
X-RAY DIFFRACTIONr_mcbond_other0.1722161
X-RAY DIFFRACTIONr_mcangle_it1.62138481
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.03243260
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0662478
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: 2.95→3.027 Å
RfactorNum. reflection% reflection
Rfree0.358 33 2.2 %
Rwork0.38 1984 -
obs--97.35 %

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