[English] 日本語
Yorodumi
- PDB-2le9: RAGEC2-S100A13 tetrameric complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2le9
TitleRAGEC2-S100A13 tetrameric complex
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A13
KeywordsMEMBRANE PROTEIN/METAL BINDING PROTEIN / Receptor for Advanced Glycation End products / S100A13 / tetrameric complex / MEMBRANE PROTEIN-METAL BINDING PROTEIN complex
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 / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression ...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 / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / positive regulation of interleukin-1 alpha production / transcytosis / RAGE receptor binding / induction of positive chemotaxis / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / positive regulation of p38MAPK cascade / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / regulation of long-term synaptic potentiation / negative regulation of connective tissue replacement involved in inflammatory response wound healing / regulation of spontaneous synaptic transmission / scavenger receptor activity / laminin receptor activity / mast cell degranulation / positive regulation of double-strand break repair / negative regulation of interleukin-10 production / fibroblast growth factor 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 / positive regulation of interleukin-12 production / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of NF-kappaB transcription factor activity / regulation of synaptic plasticity / positive regulation of interleukin-6 production / response to wounding / fibrillar center / cellular response to amyloid-beta / neuron projection development / calcium-dependent protein binding / positive regulation of tumor necrosis factor production / cell junction / transmembrane signaling receptor activity / protein transport / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / molecular adaptor activity / histone binding / response to hypoxia / learning or memory / early endosome / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / apical plasma membrane / inflammatory response / copper ion binding / lipid binding / calcium ion binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / DNA binding / extracellular space / RNA binding / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 / Immunoglobulin domain / EF-hand / Recoverin; domain 1 ...: / 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 / Immunoglobulin domain / EF-hand / Recoverin; domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Advanced glycosylation end product-specific receptor / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsRani, S.G. / Mohan, S.K. / Yu, C.
CitationJournal: To be Published
Title: Interaction of S100A13 with Receptor for Advanced Glycation End products (RAGE) C2 domain
Authors: Rani, S.G. / Mohan, S.K. / Yu, C.
History
DepositionJun 14, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2Oct 9, 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
A: Advanced glycosylation end product-specific receptor
B: Protein S100-A13
C: Protein S100-A13
D: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)42,0104
Polymers42,0104
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)1 / 4000structures with the lowest energy
Representative

-
Components

#1: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 9645.792 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 235-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE, RAGEC2 / Variant: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q15109
#2: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11358.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Variant: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q99584
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
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 C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D 13C-Filter NOESY
21322D 1H-15N HSQC
21423D HNCA
21523D HN(CO)CA
21623D HN(CA)CB
21723D CBCA(CO)NH
21823D C(CO)NH
21923D H(CCO)NH
22023D HBHA(CO)NH
22123D 1H-15N NOESY
22223D 1H-13C NOESY
22323D HNCO
224213C Filter NOESY
12513D HNCO

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.1 mM entity_2-2, 25 mM sodium phosphate-3, 100 mM sodium chloride-4, 1 mM DTT-5, 0.02 mM sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM entity_1-7, 1.2 mM [U-100% 13C; U-100% 15N] entity_2-8, 25 mM sodium phosphate-9, 100 mM sodium chloride-10, 1 mM DTT-11, 0.02 mM sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMentity_1-1[U-100% 13C; U-100% 15N]1
1.1 mMentity_2-21
25 mMsodium phosphate-31
100 mMsodium chloride-41
1 mMDTT-51
0.02 mMsodium azide-61
1.2 mMentity_1-72
1.2 mMentity_2-8[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-92
100 mMsodium chloride-102
1 mMDTT-112
0.02 mMsodium azide-122
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11006.5ambient 298 K
21006.5ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7001
Varian INOVAVarianINOVA7002
Varian INOVAVarianINOVA7003

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2 & 2.2Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
HADDOCK2Alexandre Bonvincomplex structure
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
VNMRVariancollection
VNMRVarianprocessing
TALOSCornilescu, Delaglio and Baxdihedral angles
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 1 / 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