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- PDB-7e4b: Crystal structure of MIF bound to compound 5 -

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Basic information

Entry
Database: PDB / ID: 7e4b
TitleCrystal structure of MIF bound to compound 5
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / tautomerase / cytokine
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
Chem-MRI / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsFan, C.P. / Guo, D.Y. / Yang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Identification and Structure-Activity Relationships of Dietary Flavonoids as Human Macrophage Migration Inhibitory Factor (MIF) Inhibitors.
Authors: Yang, L. / Guo, D. / Fan, C.
History
DepositionFeb 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)37,5098
Polymers37,0653
Non-polymers4445
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-78 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.028, 68.513, 85.333
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
11(chain A and (resid 1 through 27 or (resid 28...
21(chain B and (resid 1 through 34 or resid 36...
31(chain C and (resid 1 through 27 or (resid 28...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 271 - 27
12GLNGLNGLNGLN(chain A and (resid 1 through 27 or (resid 28...AA2828
13PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 1141 - 114
14PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 1141 - 114
15PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 1141 - 114
16PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 1141 - 114
17PROPROALAALA(chain A and (resid 1 through 27 or (resid 28...AA1 - 1141 - 114
21PROPROPROPRO(chain B and (resid 1 through 34 or resid 36...BB1 - 341 - 34
22TYRTYRSERSER(chain B and (resid 1 through 34 or resid 36...BB36 - 7636 - 76
23LYSLYSLYSLYS(chain B and (resid 1 through 34 or resid 36...BB7777
24PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
25PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
26PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
27PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
28PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
29PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB1 - 1141 - 114
31PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 271 - 27
32GLNGLNGLNGLN(chain C and (resid 1 through 27 or (resid 28...CC2828
33PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 1141 - 114
34PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 1141 - 114
35PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 1141 - 114
36PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 1141 - 114
37PROPROALAALA(chain C and (resid 1 through 27 or (resid 28...CC1 - 1141 - 114

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MRI / 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one / Morin


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M ammonium, 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→47.543 Å / Num. obs: 38288 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.024 / Rrim(I) all: 0.076 / Rsym value: 0.072 / Net I/av σ(I): 21.6 / Net I/σ(I): 21.6
Reflection shellResolution: 1.77→1.81 Å / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2101 / CC1/2: 0.666 / Rpim(I) all: 0.457 / Rrim(I) all: 1.456 / Rsym value: 1.38 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.772→47.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1916 5.01 %
Rwork0.2014 36313 -
obs0.203 38229 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.29 Å2 / Biso mean: 30.7127 Å2 / Biso min: 14.95 Å2
Refinement stepCycle: final / Resolution: 1.772→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 26 234 2846
Biso mean--27.46 37.23 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012677
X-RAY DIFFRACTIONf_angle_d1.0373650
X-RAY DIFFRACTIONf_chiral_restr0.067402
X-RAY DIFFRACTIONf_plane_restr0.008479
X-RAY DIFFRACTIONf_dihedral_angle_d8.8851795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1520X-RAY DIFFRACTION5.702TORSIONAL
12B1520X-RAY DIFFRACTION5.702TORSIONAL
13C1520X-RAY DIFFRACTION5.702TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7722-1.81660.49621300.4303250999
1.8166-1.86570.32481340.33592555100
1.8657-1.92060.32091360.30092557100
1.9206-1.98260.33431380.27292569100
1.9826-2.05340.24681310.22512569100
2.0534-2.13560.27261360.21872576100
2.1356-2.23280.26751370.2182559100
2.2328-2.35060.27021340.21882588100
2.3506-2.49780.25991300.19572589100
2.4978-2.69070.23781410.21072585100
2.6907-2.96140.23171360.21572623100
2.9614-3.38980.22561410.19032609100
3.3898-4.27040.17961390.15092665100
4.2704-47.540.18831530.17422760100
Refinement TLS params.Method: refined / Origin x: 88.3864 Å / Origin y: 74.0975 Å / Origin z: 10.4913 Å
111213212223313233
T0.2138 Å2-0.0121 Å2-0.01 Å2-0.1596 Å20.0107 Å2--0.1644 Å2
L1.7666 °2-0.4146 °20.444 °2-1.673 °2-0.6325 °2--1.5912 °2
S0.067 Å °-0.0974 Å °-0.1712 Å °0.0973 Å °0.0063 Å °0.0941 Å °0.1806 Å °-0.017 Å °-0.0469 Å °
Refinement TLS groupSelection details: all

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