[English] 日本語
Yorodumi
- PDB-2m1k: Interaction of Human S100A6 (C3S) with V domain of Receptor for A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m1k
TitleInteraction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products (RAGE)
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A6
KeywordsPROTEIN BINDING / S100A6 C3S / RAGE V / heterotetrameric / HADDOCK model
Function / homology
Function and homology information


advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation ...advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / monoatomic ion transmembrane transporter activity / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / transcytosis / induction of positive chemotaxis / positive regulation of heterotypic cell-cell adhesion / positive regulation of monocyte chemotactic protein-1 production / S100 protein binding / positive regulation of p38MAPK cascade / regulation of long-term synaptic potentiation / protein localization to membrane / regulation of spontaneous synaptic transmission / negative regulation of connective tissue replacement involved in inflammatory response wound healing / scavenger receptor activity / laminin receptor activity / negative regulation of interleukin-10 production / positive regulation of double-strand break repair / tropomyosin binding / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / phagocytosis / phagocytic cup / transport across blood-brain barrier / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / astrocyte activation / axonogenesis / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / positive regulation of interleukin-6 production / response to wounding / cytoplasmic side of plasma membrane / fibrillar center / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / neuron projection development / positive regulation of tumor necrosis factor production / calcium-dependent protein binding / cell junction / transmembrane signaling receptor activity / nuclear envelope / signaling receptor activity / : / amyloid-beta binding / regulation of inflammatory response / histone binding / molecular adaptor activity / learning or memory / early endosome / response to hypoxia / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / apical plasma membrane / inflammatory response / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / signal transduction / protein homodimerization activity / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein S100-A6 / : / 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 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain ...Protein S100-A6 / : / 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 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / EF-hand / Recoverin; domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein S100-A6 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGupta, A.A. / Yu, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Interaction of the S100A6 mutant (C3S) with the V domain of the receptor for advanced glycation end products (RAGE).
Authors: Mohan, S.K. / Gupta, A.A. / Yu, C.
History
DepositionNov 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein S100-A6
D: Protein S100-A6
A: Advanced glycosylation end product-specific receptor
C: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)42,7894
Polymers42,7894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area23380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein S100-A6 / Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / ...Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / PRA / S100 calcium-binding protein A6


Mass: 10177.664 Da / Num. of mol.: 2 / Mutation: C3S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACY, S100A6 / Plasmid: pET(20b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06703
#2: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 11217.007 Da / Num. of mol.: 2 / Fragment: UNP residues 23-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pET(15b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15109
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D HCACO

-
Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] S100A6 C3S, 20 mM TRIS, 10 mM Calcium chloride, 0.01 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMS100A6 C3S-1[U-100% 13C; U-100% 15N]1
20 mMTRIS-21
10 mMCalcium chloride-31
0.01 %sodium azide-41
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3Variancollection
VnmrJ2.3Varianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: HADDOCK STARTING STRUCTURES ARE PDB ENTRIES 1K9K AND 2E5E. MODELS 1-10 ARE SUPERIMPOSED, WHILE MODELS 11-20 ARE SUPERIMPOSED IN A DIFFERENT ORIENTATION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 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