[English] 日本語
Yorodumi
- EMDB-35276: The RAGE and HMGB1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35276
TitleThe RAGE and HMGB1 complex
Map data
Sample
  • Complex: The RAGE and HMGB1 complex
    • Protein or peptide: High mobility group protein B1
    • Protein or peptide: Advanced glycosylation end product-specific receptor
KeywordsRAGE / HMGB1 / Inflammation / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / negative regulation of apoptotic cell clearance / advanced glycation end-product receptor activity / positive regulation of endothelin production / negative regulation of RNA polymerase II transcription preinitiation complex assembly ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / negative regulation of apoptotic cell clearance / advanced glycation end-product receptor activity / positive regulation of endothelin production / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / regulation of T cell mediated cytotoxicity / myeloid dendritic cell activation / glucose mediated signaling pathway / T-helper 1 cell activation / negative regulation of long-term synaptic depression / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / regulation of p38MAPK cascade / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / regulation of non-canonical NF-kappaB signal transduction / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / Regulation of TLR by endogenous ligand / scavenger receptor activity / alphav-beta3 integrin-HMGB1 complex / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / transcytosis / protein localization to membrane / Apoptosis induced DNA fragmentation / positive regulation of monocyte chemotactic protein-1 production / inflammatory response to antigenic stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / supercoiled DNA binding / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / apoptotic cell clearance / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / dendritic cell chemotaxis / laminin receptor activity / positive regulation of p38MAPK cascade / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to amyloid-beta / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / negative regulation of blood vessel endothelial cell migration / negative regulation of type II interferon production / transport across blood-brain barrier / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of long-term synaptic potentiation / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / Pyroptosis / positive regulation of autophagy / heterochromatin formation / DNA polymerase binding / four-way junction DNA binding / positive regulation of chemokine production / condensed chromosome / positive regulation of interleukin-12 production / activation of innate immune response / transcription repressor complex / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / lipopolysaccharide binding / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / autophagy / response to wounding / double-strand break repair via nonhomologous end joining / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / transcription corepressor activity
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / HMG-box domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / HMG-box domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Similarity search - Domain/homology
High mobility group protein B1 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.19 Å
AuthorsHan CW / Kim HJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The RAGE and HMGB1 complex
Authors: Han CW / Kim HJ
History
DepositionFeb 7, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35276.png

Downloads & links

-
Map

FileDownload / File: emd_35276.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.967 Å
Density
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-1.8844837 - 4.84788
Average (Standard dev.)0.000023142018 (±0.07198738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 393.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_35276_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35276_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35276_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The RAGE and HMGB1 complex

EntireName: The RAGE and HMGB1 complex
Components
  • Complex: The RAGE and HMGB1 complex
    • Protein or peptide: High mobility group protein B1
    • Protein or peptide: Advanced glycosylation end product-specific receptor

-
Supramolecule #1: The RAGE and HMGB1 complex

SupramoleculeName: The RAGE and HMGB1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

-
Macromolecule #1: High mobility group protein B1

MacromoleculeName: High mobility group protein B1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.590859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FKDPNAPKRP PSAFFLFCSE YRPKIKGEHP GLSIGDVAKK LGEMWNNTAA DDKQPYEKKA AKLKEKYEKD IAAYR

UniProtKB: High mobility group protein B1

-
Macromolecule #2: Advanced glycosylation end product-specific receptor

MacromoleculeName: Advanced glycosylation end product-specific receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.068414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AQNITARIGE PLVLKCKGAP KKPPQRLEWK LNTGRTEAWK VLSPQGGGPW DSVARVLPNG SLFLPAVGIQ DEGIFRCQAM NRNGKETKS NYRVRVYQIP GKPEIVDSAS ELTAGVPNKV GTCVSEGSYP AGTLSWHLDG KPLVPNEKGV SVKEQTRRHP E TGLFTLQS ...String:
AQNITARIGE PLVLKCKGAP KKPPQRLEWK LNTGRTEAWK VLSPQGGGPW DSVARVLPNG SLFLPAVGIQ DEGIFRCQAM NRNGKETKS NYRVRVYQIP GKPEIVDSAS ELTAGVPNKV GTCVSEGSYP AGTLSWHLDG KPLVPNEKGV SVKEQTRRHP E TGLFTLQS ELMVTPARGG DPRPTFSCSF SPGLPRHRAL RTAPIQPRVW EPV

UniProtKB: Advanced glycosylation end product-specific receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2yrq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121467
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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://pdbjlvh1.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