[English] 日本語
Yorodumi
- PDB-1k9c: Solution Structure of Calreticulin P-domain subdomain (residues 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k9c
TitleSolution Structure of Calreticulin P-domain subdomain (residues 189-261)
ComponentsCALRETICULIN
KeywordsMETAL TRANSPORT / HAIRPIN
Function / homology
Function and homology information


response to biphenyl / Scavenging by Class A Receptors / Calnexin/calreticulin cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / response to peptide / cortical granule ...response to biphenyl / Scavenging by Class A Receptors / Calnexin/calreticulin cycle / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / cytolytic granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / response to peptide / cortical granule / cellular response to electrical stimulus / complement component C1q complex binding / regulation of meiotic nuclear division / negative regulation of retinoic acid receptor signaling pathway / response to glycoside / endoplasmic reticulum quality control compartment / sarcoplasmic reticulum lumen / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / molecular sequestering activity / cortical actin cytoskeleton organization / nuclear androgen receptor binding / cellular response to lithium ion / response to testosterone / protein localization to nucleus / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of cell cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / ERAD pathway / protein export from nucleus / positive regulation of endothelial cell migration / acrosomal vesicle / sarcoplasmic reticulum / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / cellular senescence / unfolded protein binding / integrin binding / protein folding / response to estradiol / nuclear envelope / carbohydrate binding / spermatogenesis / collagen-containing extracellular matrix / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of DNA-templated transcription / mRNA binding / glutamatergic synapse / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Calnexin lumenal domain, non-globular proline-rich hairpin domain / Calreticulin/calnexin, P domain / Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. ...Calnexin lumenal domain, non-globular proline-rich hairpin domain / Calreticulin/calnexin, P domain / Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Ribbon / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsEllgaard, L. / Bettendorff, P. / Braun, D. / Herrmann, T. / Fiorito, F. / Guntert, P. / Helenius, A. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: NMR Structures of 36 and 73-residue Fragments of the Calreticulin P-domain
Authors: Ellgaard, L. / Bettendorff, P. / Braun, D. / Herrmann, T. / Fiorito, F. / Jelesarov, I. / Guntert, P. / Helenius, A. / Wuthrich, K.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALRETICULIN


Theoretical massNumber of molelcules
Total (without water)8,7811
Polymers8,7811
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)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein CALRETICULIN / CRP55 / CALREGULIN / HACBP / ERP60 / CALBP / CALCIUM-BINDING PROTEIN 3 / CABP3


Mass: 8781.471 Da / Num. of mol.: 1 / Fragment: P-DOMAIN, RESIDUES 189-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P18418

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D combined 13C/15N-separated NOESY
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D ct-(H)CCH-TOCSY

-
Sample preparation

DetailsContents: 3 mM CALRETICULIN P-DOMAIN SUBDOMAIN; 10 mM CaCl2; 95% H20; 5% D20
Solvent system: 95% H20; 5% D20
Sample conditionsIonic strength: 10 mM CaCl2 / pH: 6.3 / Pressure: ambient / Temperature: 293.4 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX8003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
DYANA1.68Guentertstructure solution
DYANA1.68Guentertrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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