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- PDB-3ijj: Ternary Complex of Macrophage Migration Inhibitory Factor (MIF) B... -

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Basic information

Entry
Database: PDB / ID: 3ijj
TitleTernary Complex of Macrophage Migration Inhibitory Factor (MIF) Bound Both to 4-hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-stereoisomer)
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / allosteric inhibition / Cytokine / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Secreted
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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / 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 lipopolysaccharide-mediated signaling pathway / 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 / protein homotrimerization / chemoattractant activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / innate immune response / negative regulation of gene expression / 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 / cytosol / cytoplasm
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AVR / Chem-EN1 / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsCrichlow, G.V. / Cho, Y. / Lolis, E.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast.
Authors: Cho, Y. / Crichlow, G.V. / Vermeire, J.J. / Leng, L. / Du, X. / Hodsdon, M.E. / Bucala, R. / Cappello, M. / Gross, M. / Gaeta, F. / Johnson, K. / Lolis, E.J.
History
DepositionAug 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)38,66118
Polymers37,0653
Non-polymers1,59615
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-104 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.236, 67.908, 87.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA2 - 152 - 15
21METMETPROPROBB2 - 152 - 15
31METMETPROPROCC2 - 152 - 15
12GLYGLYPROPROAA17 - 3417 - 34
22GLYGLYPROPROBB17 - 3417 - 34
32GLYGLYPROPROCC17 - 3417 - 34
13ALAALAALAALAAA38 - 11438 - 114
23ALAALAALAALABB38 - 11438 - 114
33ALAALAALAALACC38 - 11438 - 114

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLIF, MIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

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Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-EN1 / (2E)-2-hydroxy-3-(4-hydroxyphenyl)prop-2-enoic acid


Mass: 180.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8O4
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AVR / (2R)-2-amino-1-[2-(1-methylethyl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one / (R)-2-amino-1-(2-isopropylpyrazolo[1,5-a]pyridin-3-yl)propan-1-one


Mass: 231.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMOLECULE ENO 901 CHAIN C COULD NOT BE THE ENOL TAUTOMER, DUE TO THE DIHEDRAL ANGLE BETWEEN C2 AND ...MOLECULE ENO 901 CHAIN C COULD NOT BE THE ENOL TAUTOMER, DUE TO THE DIHEDRAL ANGLE BETWEEN C2 AND C3 OF THE PYRUVATE NOT ALLOWING A DOUBLE BOND, BUT WITH THE BOND ANGLE AT ATOM C3 TOO WIDE FOR THE KETO TAUTOMER. THEREFORE, ACCORDING TO THE ELECTRON DENSITY (WHICH HAS HIGH RESOLUTION) IT WOULD APPEAR AS IF IT IS SOME FORM OF INTERMEDIATE.

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 3% isopropanol, 0.5 M NaCl, 0.1 M tris(hydroxymethyl)aminomethane; mixed in a 1:1 ratio with the protein:substrate:inhibitor complex, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2009 / Details: mirror and monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 1.25→100 Å / Num. obs: 110659 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.334 / Net I/σ(I): 16.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.475 / Num. unique all: 5484 / Χ2: 0.926 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.357 / Cor.coef. Fo:Fc: 0.677 / Cor.coef. Io to Ic: 0.6
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3DJH

3djh


Resolution: 1.25→53.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.905 / SU R Cruickshank DPI: 0.041 / SU Rfree: 0.04 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1117 1 %RANDOM
Rwork0.162 ---
obs0.163 110630 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.96 Å2 / Biso mean: 16.909 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.041 Å
Refinement stepCycle: LAST / Resolution: 1.25→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 103 479 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222815
X-RAY DIFFRACTIONr_angle_refined_deg1.2012.013844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21624.074108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3715422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8321513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0310.0212184
X-RAY DIFFRACTIONr_mcbond_it2.4631.51756
X-RAY DIFFRACTIONr_mcangle_it3.84222846
X-RAY DIFFRACTIONr_scbond_it4.84831059
X-RAY DIFFRACTIONr_scangle_it7.0364.5992
X-RAY DIFFRACTIONr_rigid_bond_restr1.69532815
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 769 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.185
BLOOSE POSITIONAL0.275
CLOOSE POSITIONAL0.225
ALOOSE THERMAL3.1210
BLOOSE THERMAL4.3310
CLOOSE THERMAL3.8810
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 79 -
Rwork0.243 7910 -
all-7989 -
obs--98.14 %

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