[English] 日本語
Yorodumi
- PDB-7xtx: High resolution crystal structure of human macrophage migration i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xtx
TitleHigh resolution crystal structure of human macrophage migration inhibitory factor in complex with methotrexate
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE/INHIBITOR / methotrexate / cytokine-inhibitor complex
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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic 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 peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / 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 / 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
ISOPROPYL ALCOHOL / Chem-MT1 / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSugishima, K. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07011 Japan
CitationJournal: To Be Published
Title: Identification of methotrexate as an inhibitor of macrophage migration inhibitory factor by high-resolution crystal structure analysis
Authors: Sugishima, K. / Kariya, Y. / Ezawa, T. / Nagatoishi, S. / Tsumoto, K. / Shigeta, Y. / Noguchi, K. / Yohda, M. / Odaka, M. / Wakui, H. / Matsumura, H.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)38,76822
Polymers37,0653
Non-polymers1,70319
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-61 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.520, 68.284, 88.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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: 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

-
Non-polymers , 5 types, 347 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-MT1 / N-(4-{[(2,4-DIAMINOPTERIDIN-1-IUM-6-YL)METHYL](METHYL)AMINO}BENZOYL)-L-GLUTAMIC ACID / METHOTREXATE PROTONATED AT N1


Mass: 455.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0 M Ammonium sulfate 0.1 M Tris-HCl (pH 8.0) 4 % isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 104194 / % possible obs: 98.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.82 Å2 / CC1/2: 1 / Net I/σ(I): 27.4
Reflection shellResolution: 1.28→1.33 Å / Num. unique obs: 10126 / CC1/2: 0.73 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J7Q

5j7q


Resolution: 1.28→34.14 Å / SU ML: 0.1219 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3821 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.188 5339 5.13 %
Rwork0.17 98770 -
obs0.1709 104109 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.55 Å2
Refinement stepCycle: LAST / Resolution: 1.28→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 109 328 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532908
X-RAY DIFFRACTIONf_angle_d0.80143967
X-RAY DIFFRACTIONf_chiral_restr0.0875429
X-RAY DIFFRACTIONf_plane_restr0.0059522
X-RAY DIFFRACTIONf_dihedral_angle_d7.3731629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.27011630.27212849X-RAY DIFFRACTION85.91
1.29-1.310.27811780.24643210X-RAY DIFFRACTION97.89
1.31-1.320.25391810.23683316X-RAY DIFFRACTION99.29
1.32-1.340.24261780.23583297X-RAY DIFFRACTION99.37
1.34-1.360.22271520.22053310X-RAY DIFFRACTION99.23
1.36-1.380.21521710.20973287X-RAY DIFFRACTION98.77
1.38-1.40.23471920.20963281X-RAY DIFFRACTION99.09
1.4-1.420.24121610.19993299X-RAY DIFFRACTION98.89
1.42-1.440.1951850.19443271X-RAY DIFFRACTION98.63
1.44-1.460.2341680.18593288X-RAY DIFFRACTION98.83
1.46-1.490.19151480.17823301X-RAY DIFFRACTION98.26
1.49-1.520.16851910.17273270X-RAY DIFFRACTION98.13
1.52-1.540.20061960.16673249X-RAY DIFFRACTION98.26
1.54-1.580.17881750.17073284X-RAY DIFFRACTION97.91
1.58-1.610.16961940.16543279X-RAY DIFFRACTION98.83
1.61-1.650.19161690.15723275X-RAY DIFFRACTION98.29
1.65-1.690.16831820.15523298X-RAY DIFFRACTION98.36
1.69-1.740.15581750.163280X-RAY DIFFRACTION98.04
1.74-1.790.20871930.15653232X-RAY DIFFRACTION97.69
1.79-1.840.18831930.16123279X-RAY DIFFRACTION97.75
1.84-1.910.16161720.15643280X-RAY DIFFRACTION97.79
1.91-1.990.1642170.15893237X-RAY DIFFRACTION97.76
1.99-2.080.17791780.1593291X-RAY DIFFRACTION97.61
2.08-2.190.17281860.15763303X-RAY DIFFRACTION97.79
2.19-2.320.15531400.1583348X-RAY DIFFRACTION98.06
2.32-2.50.19081750.17583358X-RAY DIFFRACTION99.05
2.5-2.750.20271790.17943390X-RAY DIFFRACTION99.69
2.75-3.150.2071800.17893425X-RAY DIFFRACTION99.97
3.15-3.970.16581890.15763469X-RAY DIFFRACTION99.95
3.97-34.140.20041780.16493514X-RAY DIFFRACTION97.23

+
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