[English] 日本語
Yorodumi
- PDB-1fim: MACROPHAGE MIGRATION INHIBITORY FACTOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fim
TitleMACROPHAGE MIGRATION INHIBITORY FACTOR
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsCYTOKINE / MACROPHAGE / INFLAMMATORY RESPONSE
Function / homology
Function and homology information


response to menaquinone / Cell surface interactions at the vascular wall / brain renin-angiotensin system / : / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / positive regulation of axon regeneration / phenylpyruvate tautomerase activity ...response to menaquinone / Cell surface interactions at the vascular wall / brain renin-angiotensin system / : / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / positive regulation of axon regeneration / phenylpyruvate tautomerase activity / positive regulation of acute inflammatory response / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / drinking behavior / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / carboxylic acid metabolic process / positive regulation of potassium ion transport / positive regulation of arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / prostaglandin biosynthetic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / Neutrophil degranulation / positive regulation of smooth muscle cell migration / skin development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to vitamin E / 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 / hair follicle development / positive regulation of phosphorylation / response to mechanical stimulus / positive regulation of B cell proliferation / response to progesterone / response to hormone / response to glucocorticoid / negative regulation of cell migration / cytokine activity / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of D-glucose import across plasma membrane / DNA damage response, signal transduction by p53 class mediator / response to insulin / positive regulation of immune response / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / cellular senescence / response to estradiol / regulation of cell population proliferation / protease binding / spermatogenesis / response to lipopolysaccharide / cellular response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / response to xenobiotic stimulus / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex binding / cell surface / : / 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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSuzuki, M. / Sugimoto, H. / Nakagawa, A. / Tanaka, I.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of the macrophage migration inhibitory factor from rat liver.
Authors: Suzuki, M. / Sugimoto, H. / Nakagawa, A. / Tanaka, I. / Nishihira, J. / Sakai, M.
#1: Journal: J.Struct.Biol. / Year: 1995
Title: Crystallization of Rat Liver Macrophage Migration Inhibitory Factor for MAD Analysis
Authors: Sugimoto, H. / Suzuki, M. / Nakagawa, A. / Tanaka, I. / Fujinaga, M. / Nishihira, J.
History
DepositionJan 31, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)12,2831
Polymers12,2831
Non-polymers00
Water00
1
A: MACROPHAGE MIGRATION INHIBITORY FACTOR

A: MACROPHAGE MIGRATION INHIBITORY FACTOR

A: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)36,8483
Polymers36,8483
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Unit cell
Length a, b, c (Å)61.800, 61.800, 53.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR


Mass: 12282.658 Da / Num. of mol.: 1 / Mutation: M2A, M101A
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONYL PROTEIN (MET 47) / Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: METHIONINE AUXOTROPIC ESCHERICHIA COLI STRAINS HARVESTED IN A MEDIUM CONTAINING SELENOMETHIONINE
Organ: LIVER / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30904
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate1reservoir
20.1 MMES1reservoir
310 %dioxane1reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 283 K
DetectorDate: May 18, 1995
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 5697 / % possible obs: 94.5 % / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.2→5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -3.59 %
Rwork0.197 --
obs0.197 5143 94.6 %
Displacement parametersBiso mean: 30.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 0 0 782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.718
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.88
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.602
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.886
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.602

+
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