[English] 日本語
Yorodumi
- PDB-2n6f: Structure of Pleiotrophin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n6f
TitleStructure of Pleiotrophin
ComponentsPleiotrophin
KeywordsHeparin-binding Protein / cytokine / glycosaminoglycan-binding protein / mitogen / angiogenesis
Function / homology
Function and homology information


dendrite regeneration / ossification involved in bone remodeling / cell surface receptor protein tyrosine phosphatase signaling pathway / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding / regulation of stem cell population maintenance / regulation of endothelial cell migration / dendrite arborization / positive regulation of stem cell differentiation / response to auditory stimulus ...dendrite regeneration / ossification involved in bone remodeling / cell surface receptor protein tyrosine phosphatase signaling pathway / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding / regulation of stem cell population maintenance / regulation of endothelial cell migration / dendrite arborization / positive regulation of stem cell differentiation / response to auditory stimulus / tissue regeneration / positive regulation of ossification / positive regulation of hepatocyte proliferation / positive regulation of dendrite development / positive regulation of leukocyte chemotaxis / protein phosphatase inhibitor activity / regulation of myelination / negative regulation of neuroblast proliferation / regulation of hemopoiesis / oogenesis / positive regulation of oligodendrocyte differentiation / Signaling by ALK / positive regulation of axon regeneration / bone mineralization / receptor clustering / positive regulation of cell division / decidualization / negative regulation of long-term synaptic potentiation / estrous cycle / positive regulation of bone mineralization / learning / molecular function activator activity / integrin-mediated signaling pathway / growth factor activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / memory / positive regulation of neuron projection development / integrin binding / heparin binding / nervous system development / carbohydrate binding / positive regulation of cell population proliferation / protein kinase binding / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular region / plasma membrane
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsRyan, E.O. / Shen, D. / Wang, X.
CitationJournal: Febs J. / Year: 2016
Title: Structural studies reveal an important role for the pleiotrophin C-terminus in mediating interactions with chondroitin sulfate.
Authors: Ryan, E. / Shen, D. / Wang, X.
History
DepositionAug 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pleiotrophin


Theoretical massNumber of molelcules
Total (without water)15,3471
Polymers15,3471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Pleiotrophin / PTN / Heparin-binding brain mitogen / HBBM / Heparin-binding growth factor 8 / HBGF-8 / Heparin- ...PTN / Heparin-binding brain mitogen / HBBM / Heparin-binding growth factor 8 / HBGF-8 / Heparin-binding growth-associated molecule / HB-GAM / Heparin-binding neurite outgrowth-promoting factor 1 / HBNF-1 / Osteoblast-specific factor 1 / OSF-1


Mass: 15346.931 Da / Num. of mol.: 1 / Fragment: UNP residues 33-168
Source method: isolated from a genetically manipulated source
Details: Two domains connected by a flexible linker / Source: (gene. exp.) Homo sapiens (human) / Gene: HBNF1, NEGF1, PTN / Production host: Escherichia coli (E. coli) / Strain (production host): Origami BL21(DE3) / References: UniProt: P21246

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution Structure of Pleiotrophin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] PTN, 10 % v/v D2O, 10 mM MES, 150 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMPTN-1[U-100% 13C; U-100% 15N]1
10 v/vD2O-21
10 mMMES-31
150 mMsodium chloride-41
Sample conditionsIonic strength: 0.15 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement with the default protocol
NMR constraintsNOE constraints total: 749 / NOE intraresidue total count: 263 / NOE long range total count: 147 / NOE medium range total count: 44 / NOE sequential total count: 295 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 62
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 0.9 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 9 ° / Maximum upper distance constraint violation: 0.73 Å
NMR ensemble rmsDistance rms dev: 0.08 Å

+
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