[English] 日本語
Yorodumi
- PDB-1sym: 3-D SOLUTION STRUCTURE OF REDUCED APO-S100B FROM RAT, NMR, 20 STR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sym
Title3-D SOLUTION STRUCTURE OF REDUCED APO-S100B FROM RAT, NMR, 20 STRUCTURES
ComponentsS100B
KeywordsCALCIUM-BINDING PROTEIN / METAL-BINDING
Function / homology
Function and homology information


TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of skeletal muscle cell differentiation / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / astrocyte differentiation / response to methylmercury ...TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of skeletal muscle cell differentiation / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / astrocyte differentiation / response to methylmercury / S100 protein binding / neuron projection extension / response to anesthetic / regulation of neuronal synaptic plasticity / positive regulation of synaptic transmission / ruffle / positive regulation of neuron differentiation / response to glucocorticoid / tau protein binding / memory / long-term synaptic potentiation / calcium-dependent protein binding / regulation of cell shape / response to ethanol / cellular response to hypoxia / learning or memory / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / ciliary basal body / positive regulation of apoptotic process / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsDrohat, A.C. / Weber, D.J.
Citation
Journal: Biochemistry / Year: 1996
Title: Solution structure of rat apo-S100B(beta beta) as determined by NMR spectroscopy.
Authors: Drohat, A.C. / Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Baldisseri, D. / Weber, D.J.
#1: Journal: J.Biomol.NMR / Year: 1995
Title: 1H, 13C and 15N NMR Assignments and Solution Secondary Structure of Rat Apo-S100 Beta
Authors: Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Shah, S. / Hilt, D.C. / Weber, D.J.
History
DepositionMay 29, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: S100B
B: S100B


Theoretical massNumber of molelcules
Total (without water)21,5162
Polymers21,5162
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 / -
Representative

-
Components

#1: Protein S100B / S100B(BETABETA) / S100BETA / S100(BETABETA)


Mass: 10758.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SYMMETRIC DIMER OF APO-S100BETA SUBUNITS, JOINED BY NONCOVALENT INTERACTION AT THE DIMER INTERFACE
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100BETA FROM RATTUS NORVEGICU / Plasmid: PET11B / Gene (production host): S100BETA FROM RATTUS NORVEGICUS / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P04631

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers 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