[English] 日本語
Yorodumi
- PDB-1mkn: N-TERMINAL HALF OF MIDKINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mkn
TitleN-TERMINAL HALF OF MIDKINE
ComponentsPROTEIN (MIDKINE)
KeywordsHEPARIN-BINDING GROWTH FACTOR
Function / homology
Function and homology information


defecation / cerebellar granular layer development / positive regulation of inflammatory response to wounding / positive regulation of neutrophil extravasation / regulation of chondrocyte differentiation / glial cell projection elongation / positive regulation of smooth muscle cell chemotaxis / positive regulation of artery morphogenesis / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding ...defecation / cerebellar granular layer development / positive regulation of inflammatory response to wounding / positive regulation of neutrophil extravasation / regulation of chondrocyte differentiation / glial cell projection elongation / positive regulation of smooth muscle cell chemotaxis / positive regulation of artery morphogenesis / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding / positive regulation of leukocyte cell-cell adhesion / positive regulation of keratinocyte proliferation / positive regulation of cartilage development / regulation of bone remodeling / regulation of behavior / negative regulation of inflammatory response to wounding / MDK and PTN in ALK signaling / negative regulation of regulatory T cell differentiation / response to auditory stimulus / T cell activation involved in immune response / positive regulation of blood vessel branching / tissue regeneration / positive regulation of neuron migration / short-term memory / positive regulation of leukocyte chemotaxis / negative regulation of epithelial cell apoptotic process / dentate gyrus development / negative regulation of cell adhesion / positive regulation of neural precursor cell proliferation / heparan sulfate binding / negative regulation of ossification / positive regulation of neutrophil chemotaxis / positive regulation of hepatocyte proliferation / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of vascular endothelial cell proliferation / positive regulation of T cell differentiation / negative regulation of cardiac muscle cell apoptotic process / adrenal gland development / Signaling by ALK / positive regulation of oligodendrocyte differentiation / oogenesis / positive regulation of macrophage chemotaxis / positive regulation of cell division / estrous cycle / behavioral fear response / positive regulation of epithelial to mesenchymal transition / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / positive regulation of interleukin-12 production / NOTCH2 Activation and Transmission of Signal to the Nucleus / positive regulation of cell adhesion / growth factor activity / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / positive regulation of neuron projection development / response to wounding / positive regulation of inflammatory response / heparin binding / nervous system development / negative regulation of neuron apoptotic process / cell differentiation / intracellular signal transduction / positive regulation of cell migration / positive regulation of DNA-templated transcription / signal transduction / extracellular region
Similarity search - Function
Heparin-binding Growth Factor, Midkine; Chain A / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily ...Heparin-binding Growth Factor, Midkine; Chain A / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily / Pleiotrophin/Midkine, C-terminal domain superfamily / PTN/MK heparin-binding protein family, C-terminal domain / PTN/MK heparin-binding protein family, N-terminal domain / Pleiotrophin / midkine family / Single Sheet / Mainly Beta
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry
AuthorsIwasaki, W. / Nagata, K. / Hatanaka, H. / Ogura, K. / Inui, T. / Kimura, T. / Muramatsu, T. / Yoshida, K. / Tasumi, M. / Inagaki, F.
CitationJournal: EMBO J. / Year: 1997
Title: Solution structure of midkine, a new heparin-binding growth factor.
Authors: Iwasaki, W. / Nagata, K. / Hatanaka, H. / Inui, T. / Kimura, T. / Muramatsu, T. / Yoshida, K. / Tasumi, M. / Inagaki, F.
History
DepositionMar 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (MIDKINE)


Theoretical massNumber of molelcules
Total (without water)6,4881
Polymers6,4881
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)1 / -
Representative

-
Components

#1: Protein PROTEIN (MIDKINE)


Mass: 6488.487 Da / Num. of mol.: 1 / Fragment: N-TERMINAL HALF / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: P21741
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: MEAN STRUCTURE.

-
Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS 600 / Manufacturer: Varian / Model: UNITYPLUS 600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

+
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