[English] 日本語
Yorodumi
- PDB-9jiy: Macrophage migration inhibitory factor S61H/Y100H mutant complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jiy
TitleMacrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H)-L)
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE / Macrophage migration inhibitory factor
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 / chemoattractant activity / protein homotrimerization / 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 / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / vesicle / secretory granule lumen / 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 / 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) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
CARBONATE ION / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHimiyama, T. / Okamoto, Y.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX1913 Japan
Japan Science and TechnologyJPMJPR22A4 Japan
Japan Science and TechnologyJPMJFR212H Japan
Japan Society for the Promotion of Science (JSPS)21H05118 Japan
Japan Society for the Promotion of Science (JSPS)24K08609 Japan
CitationJournal: Nat Commun / Year: 2025
Title: A cytokine-based designer enzyme with an abiological multinuclear metal center exhibits intrinsic and extrinsic catalysis
Authors: Ueno, A. / Takida, F. / Kita, T. / Ishii, T. / Himiyama, T. / Mabuchi, T. / Okamoto, Y.
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)38,82219
Polymers37,5373
Non-polymers1,28516
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-202 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.153, 68.211, 86.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ABC

#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: 12512.295 Da / Num. of mol.: 3 / Mutation: S61H/Y100H
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

-
Non-polymers , 6 types, 407 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→48.22 Å / Num. obs: 126809 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.6
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6215 / CC1/2: 0.669 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→48.212 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.965 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1737 6378 5.033 %
Rwork0.1552 120353 -
all0.156 --
obs-126731 99.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.855 Å2
Baniso -1Baniso -2Baniso -3
1--0.075 Å2-0 Å2-0 Å2
2---0.053 Å2-0 Å2
3---0.128 Å2
Refinement stepCycle: LAST / Resolution: 1.2→48.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 68 391 3066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162609
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.7833807
X-RAY DIFFRACTIONr_angle_other_deg0.6361.7266001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.98515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.52510423
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.63510118
X-RAY DIFFRACTIONr_chiral_restr0.1020.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined0.2570.2514
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.22486
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21393
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2209
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0270.25
X-RAY DIFFRACTIONr_nbd_other0.1960.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.221
X-RAY DIFFRACTIONr_mcbond_it3.5341.6781410
X-RAY DIFFRACTIONr_mcbond_other3.5311.6781410
X-RAY DIFFRACTIONr_mcangle_it4.5773.0241773
X-RAY DIFFRACTIONr_mcangle_other4.5783.0241774
X-RAY DIFFRACTIONr_scbond_it7.582.0651383
X-RAY DIFFRACTIONr_scbond_other7.5782.0661384
X-RAY DIFFRACTIONr_scangle_it10.033.6242034
X-RAY DIFFRACTIONr_scangle_other10.0283.6242035
X-RAY DIFFRACTIONr_lrange_it14.42420.7413109
X-RAY DIFFRACTIONr_lrange_other13.56518.3593012
X-RAY DIFFRACTIONr_rigid_bond_restr4.55835402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.284870.27187580.27292480.9690.9799.96760.25
1.231-1.2650.2594130.23686710.23790840.9740.9781000.212
1.265-1.3020.2324300.20683810.20888130.9790.98499.97730.185
1.302-1.3420.2164750.19180790.19285560.9830.98899.97660.171
1.342-1.3850.1984290.17678400.17882760.9850.98999.91540.16
1.385-1.4340.1883730.16176690.16280440.9860.99299.97510.147
1.434-1.4880.1663690.14374110.14477800.9890.9931000.132
1.488-1.5490.1573650.12871130.12974800.990.99499.97330.121
1.549-1.6180.1583590.1268150.12171780.9880.99499.94430.116
1.618-1.6970.1673410.12565450.12768860.9870.9941000.123
1.697-1.7880.1653440.12861840.1365360.9860.99399.87760.129
1.788-1.8960.1473110.12358540.12561930.9890.99399.54790.129
1.896-2.0270.1373150.12155230.12258380.990.9921000.132
2.027-2.1890.1542920.1351790.13154730.9860.9999.96350.147
2.189-2.3980.1682630.14147540.14250290.9840.98999.76140.161
2.398-2.680.1492110.15443470.15445770.9860.98699.58490.181
2.68-3.0930.1842200.1638290.16140690.9760.98499.50850.191
3.093-3.7840.1711860.1732840.1734710.9830.98499.97120.204
3.784-5.3350.1711250.15526010.15627260.9850.9871000.188
5.335-48.2120.252700.24115160.24116090.960.96398.57050.375

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more