[English] 日本語
Yorodumi
- PDB-2jyu: Human Granulin C, isomer 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jyu
TitleHuman Granulin C, isomer 2
ComponentsGranulin-5
KeywordsCYTOKINE / Granulin C / epithelin / human / stack of hairpins / Alternative splicing / Glycoprotein / Polymorphism / Secreted
Function / homology
Function and homology information


positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response ...positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response / lysosomal transport / lysosome organization / positive regulation of axon regeneration / negative regulation of respiratory burst involved in inflammatory response / positive regulation of endothelial cell migration / cytokine activity / positive regulation of epithelial cell proliferation / growth factor activity / trans-Golgi network / positive regulation of neuron apoptotic process / positive regulation of angiogenesis / azurophil granule lumen / late endosome / regulation of inflammatory response / protein-folding chaperone binding / negative regulation of neuron apoptotic process / lysosome / protein stabilization / endosome / positive regulation of cell migration / lysosomal membrane / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / signal transduction / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Granulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTolkatchev, D. / Wang, P. / Chen, Z. / Xu, P. / Ni, F.
CitationJournal: Protein Sci. / Year: 2008
Title: Structure dissection of human progranulin identifies well-folded granulin/epithelin modules with unique functional activities.
Authors: Tolkatchev, D. / Malik, S. / Vinogradova, A. / Wang, P. / Chen, Z. / Xu, P. / Bennett, H.P. / Bateman, A. / Ni, F.
History
DepositionDec 19, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Granulin-5


Theoretical massNumber of molelcules
Total (without water)7,4021
Polymers7,4021
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 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Granulin-5 / / Granulin C


Mass: 7402.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRN / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: P28799

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
131inphase COSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
110 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 90% H2O/10% D2O90% H2O/10% D2O
210 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMsodium phosphate1
150 mMsodium chloride1
0.2 mMEDTA1
0.5 mMHgrnC21
10 mMsodium phosphate2
150 mMsodium chloride2
0.2 mMEDTA2
0.5 mMHgrnC22
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.8 ambient atm298 K
26.8 ambient atm288 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1Linge, O'Donoghue and Nilgesstructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SYBYLTriposdata analysis
Insight IIAccelrys Software Inc.data analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ARIA1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

+
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