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- PDB-7e49: Crystal structure of MIF bound to compound10 -

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Basic information

Entry
Database: PDB / ID: 7.0E+49
TitleCrystal structure of MIF bound to compound10
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / tautomerase and 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 mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / carboxylic acid metabolic process / 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 B cell proliferation / positive regulation of phosphorylation / 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 / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / 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) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
Chem-MYC / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.574 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)37,98513
Polymers37,0653
Non-polymers92010
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-124 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.756, 68.016, 88.294
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 12 or resid 14...
21(chain B and (resid 1 through 12 or resid 14...
31(chain C and (resid 1 through 12 or resid 14...

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 12 or resid 14...AA1 - 121 - 12
12VALVALALAALA(chain A and (resid 1 through 12 or resid 14...AA14 - 2714 - 27
13GLNGLNGLNGLN(chain A and (resid 1 through 12 or resid 14...AA2828
14PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
15PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
16PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
17PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
21PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 121 - 12
22VALVALTHRTHR(chain B and (resid 1 through 12 or resid 14...BB14 - 2314 - 23
23GLNGLNGLNGLN(chain B and (resid 1 through 12 or resid 14...BB2424
24PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
25PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
26PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
27PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
31PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 121 - 12
32VALVALTHRTHR(chain C and (resid 1 through 12 or resid 14...CC14 - 2314 - 23
33GLNGLNGLNGLN(chain C and (resid 1 through 12 or resid 14...CC2424
34PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
35PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
36PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
37PROPROALAALA(chain C and (resid 1 through 12 or resid 14...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 / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN / Myricetin


Mass: 318.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M ammonium sulfate, 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 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.1
ReflectionResolution: 1.57→48.002 Å / Num. obs: 57131 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Rsym value: 0.094 / Net I/av σ(I): 16.9 / Net I/σ(I): 16.9
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.703 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2636 / CC1/2: 0.47 / Rpim(I) all: 0.559 / Rrim(I) all: 1.605 / Rsym value: 1.703 / % possible all: 95.2

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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: 1.574→48 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2354 2008 3.52 %
Rwork0.2173 55012 -
obs0.2205 57062 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.91 Å2 / Biso mean: 22.1027 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: final / Resolution: 1.574→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 54 305 2941
Biso mean--26.14 28.65 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042702
X-RAY DIFFRACTIONf_angle_d0.7173688
X-RAY DIFFRACTIONf_chiral_restr0.054403
X-RAY DIFFRACTIONf_plane_restr0.006479
X-RAY DIFFRACTIONf_dihedral_angle_d8.2481827
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1515X-RAY DIFFRACTION6.145TORSIONAL
12B1515X-RAY DIFFRACTION6.145TORSIONAL
13C1515X-RAY DIFFRACTION6.145TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5752-1.61460.47491410.47743845398695
1.6146-1.65820.34061400.3893880402097
1.6582-1.7070.38891410.37193874401596
1.707-1.76210.43161420.3413883402596
1.7621-1.8250.31161400.30343883402397
1.825-1.8980.28861420.25943894403696
1.898-1.98440.24581430.23563901404496
1.9844-2.08890.23641420.22613907404996
2.0889-2.21960.24611430.21723921406496
2.2196-2.39080.21611450.21433929407496
2.3908-2.6310.22481410.22353939408097
2.631-3.01070.24111440.20673985412997
3.0107-3.78960.21331440.17544006415097
3.7896-20.99740.1721540.16554165431996
Refinement TLS params.Method: refined / Origin x: -22.2851 Å / Origin y: 7.1768 Å / Origin z: -12.0661 Å
111213212223313233
T0.103 Å2-0.0012 Å20.004 Å2-0.1028 Å2-0.0127 Å2--0.2171 Å2
L0.7128 °20.1396 °2-0.0755 °2-1.066 °2-0.5691 °2--1.4902 °2
S-0.0431 Å °0.0317 Å °-0.0493 Å °0.0206 Å °0.0006 Å °-0.1072 Å °0.0135 Å °0.0211 Å °0.0235 Å °
Refinement TLS groupSelection details: all

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