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- PDB-1emr: CRYSTAL STRUCTURE OF HUMAN LEUKEMIA INHIBITORY FACTOR (LIF) -

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Basic information

Entry
Database: PDB / ID: 1emr
TitleCRYSTAL STRUCTURE OF HUMAN LEUKEMIA INHIBITORY FACTOR (LIF)
ComponentsLEUKEMIA INHIBITORY FACTOR
KeywordsGENE REGULATION / 4-helix bundle
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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Leukemia inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsRobinson, R.C. / Heath, J.K. / Hawkins, N. / Samal, B. / Jones, E.Y. / Betzel, C.
Citation
Journal: to be published
Title: Species Variation in Receptor Binding Site Revealed by the Medium Resolution X-ray Structure of Human Leukemia Inhibitory Factor
Authors: Robinson, R.C. / Heath, J.K. / Hawkins, N. / Samal, B. / Jones, E.Y. / Betzel, C.
#1: Journal: FEBS Lett. / Year: 1993
Title: Crystallization and Preliminary X-ray Analysis of Leukemia Inhibitory Factor
Authors: Betzel, C. / Visanji, M. / Dauter, Z. / Fourme, R. / Weber, W. / Marnitz, U. / Boone, T. / Pope, J. / Miller, J. / Hawkins, N. / Samal, B.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEUKEMIA INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)17,5151
Polymers17,5151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.5, 45.3, 77.7
Angle α, β, γ (deg.)90.0, 112.3, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LEUKEMIA INHIBITORY FACTOR / LIF


Mass: 17515.262 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) / References: UniProt: P15018
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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 200 mM sodium acetate, 100 mM cacodylate buffer, 30% w/v PEG 8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 15, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionHighest resolution: 3.5 Å / Num. obs: 2728 / % possible obs: 99.4 % / Rmerge(I) obs: 0.035

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection
Rfree0.293 -
Rwork0.191 -
all-2728
obs-2728
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 0 0 1520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.25

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