[English] 日本語
Yorodumi
- PDB-1g91: SOLUTION STRUCTURE OF MYELOID PROGENITOR INHIBITORY FACTOR-1 (MPIF-1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g91
TitleSOLUTION STRUCTURE OF MYELOID PROGENITOR INHIBITORY FACTOR-1 (MPIF-1)
ComponentsMYELOID PROGENITOR INHIBITORY FACTOR-1
KeywordsCYTOKINE / chemokine / MPIF-1 / CKb8 / CCL23
Function / homology
Function and homology information


negative regulation of C-C chemokine binding / CCR1 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / Formyl peptide receptors bind formyl peptides and many other ligands / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis ...negative regulation of C-C chemokine binding / CCR1 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / Formyl peptide receptors bind formyl peptides and many other ligands / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / positive regulation of GTPase activity / cellular response to type II interferon / intracellular calcium ion homeostasis / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / G alpha (i) signalling events / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / signal transduction / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsRajarathnam, K. / Li, Y. / Rohrer, T. / Gentz, R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Solution structure and dynamics of myeloid progenitor inhibitory factor-1 (MPIF-1), a novel monomeric CC chemokine.
Authors: Rajarathnam, K. / Li, Y. / Rohrer, T. / Gentz, R.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYELOID PROGENITOR INHIBITORY FACTOR-1


Theoretical massNumber of molelcules
Total (without water)8,8691
Polymers8,8691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein MYELOID PROGENITOR INHIBITORY FACTOR-1 / MPIF-1


Mass: 8869.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): K12-DERIVED STRAIN SGI3009 / References: UniProt: P55773

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HN(CA)CB
131CBCA(CO)NH
141(H)CCH-TOCSY
2523D 15N-separated NOESY
262HNHA
3732D NOESY
383DQF-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM MPIF-1 U-13C,15N90% H2O, 10% D2O, pH 5.2
22 mM MPIF-1 U-15N90% H2O, 10% D2O, pH 5.2
32 mM MPIF-199.99 % D2O, pH 5.2
Sample conditionsIonic strength: 20 mM sodium acetate / pH: 5.2 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 711 NOE, 82 dihedral, and 36 H-bonding restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

+
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://pdbjlvh1.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