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- PDB-8ca0: Macrophage inhibitory factor (MIF) in complex with small molecule... -

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Basic information

Entry
Database: PDB / ID: 8ca0
TitleMacrophage inhibitory factor (MIF) in complex with small molecule PAV174
ComponentsMacrophage migration inhibitory factor
KeywordsPROTEIN BINDING / MIF / oxMIF / herpes / Alzheimer's disease
Function / homology
Function and homology information


positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
: / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, A. / Torres, F. / Roland, R. / Korth, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO1679/10-1, 15-1 Germany
CitationJournal: To Be Published
Title: Oxidized MIF is a drug target at the molecular intersection between immune activation and tau cellular pathology
Authors: Mueller-Schiffmann, A. / Torres, F. / Kitaygorodskyy, A. / Ramani, A. / Alatza, A. / Tschirner, S. / Prikulis, I. / Yu, S. / Dey, D. / Mallesh, S. / Prasad, D. / Solas, D. / Bader, V. / ...Authors: Mueller-Schiffmann, A. / Torres, F. / Kitaygorodskyy, A. / Ramani, A. / Alatza, A. / Tschirner, S. / Prikulis, I. / Yu, S. / Dey, D. / Mallesh, S. / Prasad, D. / Solas, D. / Bader, V. / Rozemuller, A. / Wray, S. / Gopalakrishnan, J. / Riek, R. / Lingappa, V.R. / Korth, C.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4454
Polymers37,0653
Non-polymers3801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7000 Å2
ΔGint-47 kcal/mol
Surface area14420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4target function
RepresentativeModel #1target function

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Components

#1: Protein Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-VIU / 1-ethyl-9-methyl-3,7-dipyrrolidin-1-yl-phenothiazine


Mass: 379.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1.0 mM [U-13C; U-15N] MIF, 1.0 mM PAV, 100% D2O / Label: 15N_13C_MIF / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMIF[U-13C; U-15N]1
1.0 mMPAVnatural abundance1
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
HADDOCKAlexandre Bonvin, University Utrechtrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 4 / Conformers submitted total number: 4

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