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- PDB-7n0a: Structure of Human Leukaemia Inhibitory Factor with Fab MSC1 -

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Basic information

Entry
Database: PDB / ID: 7n0a
TitleStructure of Human Leukaemia Inhibitory Factor with Fab MSC1
Components
  • Leukemia inhibitory factor
  • MSC-1 Fab Heavy chain
  • MSC-1 Fab Light chain
KeywordsCYTOKINE/IMMUNE SYSTEM / LIF / Cytokine / Antibody / Cancer therapeutics / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


leukemia inhibitory factor receptor binding / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / meiotic nuclear division / muscle organ morphogenesis / trophoblast giant cell differentiation / negative regulation of meiotic nuclear division / leukemia inhibitory factor signaling pathway / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of hormone secretion / lung vasculature development ...leukemia inhibitory factor receptor binding / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / meiotic nuclear division / muscle organ morphogenesis / trophoblast giant cell differentiation / negative regulation of meiotic nuclear division / leukemia inhibitory factor signaling pathway / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of hormone secretion / lung vasculature development / positive regulation of receptor signaling pathway via STAT / lung lobe morphogenesis / positive regulation of macrophage differentiation / positive regulation of astrocyte differentiation / IL-6-type cytokine receptor ligand interactions / cell surface receptor signaling pathway via STAT / positive regulation of cell adhesion mediated by integrin / positive regulation of peptidyl-tyrosine phosphorylation / lung alveolus development / Interleukin-10 signaling / regulation of cell differentiation / macrophage differentiation / decidualization / somatic stem cell population maintenance / blood vessel remodeling / neuron development / positive regulation of peptidyl-serine phosphorylation / embryo implantation / cytokine activity / stem cell differentiation / growth factor activity / negative regulation of ERK1 and ERK2 cascade / cell morphogenesis / positive regulation of fibroblast proliferation / fibroblast proliferation / Interleukin-4 and Interleukin-13 signaling / gene expression / response to hypoxia / positive regulation of MAPK cascade / immune response / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Leukemia inhibitory factor / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / Four-helical cytokine-like, core / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukemia inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRaman, S. / Bosch, A. / Fransson, J. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada Research Chairs950231604 Canada
CitationJournal: Clin.Cancer Res. / Year: 2023
Title: Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment.
Authors: Hallett, R.M. / Bonfill-Teixidor, E. / Iurlaro, R. / Arias, A. / Raman, S. / Bayliss, P. / Egorova, O. / Neva-Alejo, A. / McGray, A.R. / Lau, E. / Bosch, A. / Beilschmidt, M. / Maetzel, D. / ...Authors: Hallett, R.M. / Bonfill-Teixidor, E. / Iurlaro, R. / Arias, A. / Raman, S. / Bayliss, P. / Egorova, O. / Neva-Alejo, A. / McGray, A.R. / Lau, E. / Bosch, A. / Beilschmidt, M. / Maetzel, D. / Fransson, J. / Huber-Ruano, I. / Anido, J. / Julien, J.P. / Giblin, P. / Seoane, J.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Leukemia inhibitory factor
A: MSC-1 Fab Light chain
B: MSC-1 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3188
Polymers67,9763
Non-polymers1,3425
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-12 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.572, 109.380, 115.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Leukemia inhibitory factor / LIF / Differentiation-stimulating factor / D factor / Melanoma-derived LPL inhibitor / MLPLI


Mass: 19796.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIF, HILDA / Production host: Homo sapiens (human) / References: UniProt: P15018

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Antibody , 2 types, 2 molecules AB

#2: Antibody MSC-1 Fab Light chain


Mass: 24033.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody MSC-1 Fab Heavy chain


Mass: 24145.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 8 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% (v/v) isopropanol, 19% (w/v) PEG 4000, 5% (v/v) glycerol, 0.095 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332013463416 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332013463416 Å / Relative weight: 1
ReflectionResolution: 3.1→39.74 Å / Num. obs: 14528 / % possible obs: 98.4 % / Redundancy: 12 % / Biso Wilson estimate: 58.49 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.1
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 1427 / CC1/2: 0.597

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XPREPdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVH

1pvh


Resolution: 3.1→39.74 Å / SU ML: 0.4437 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 730 5.03 %
Rwork0.2318 13783 -
obs0.2345 14513 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.17 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 20 7 4755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024854
X-RAY DIFFRACTIONf_angle_d0.53386599
X-RAY DIFFRACTIONf_chiral_restr0.0383762
X-RAY DIFFRACTIONf_plane_restr0.0042841
X-RAY DIFFRACTIONf_dihedral_angle_d15.26882907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.340.33571390.29872706X-RAY DIFFRACTION99.93
3.34-3.680.33191490.26912687X-RAY DIFFRACTION99.82
3.68-4.210.32091410.24522730X-RAY DIFFRACTION99.83
4.21-5.30.25681460.20422762X-RAY DIFFRACTION99.86
5.3-39.740.23961550.20322898X-RAY DIFFRACTION99.93

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