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- EMDB-35276: The RAGE and HMGB1 complex -

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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 / calcium-dependent protein kinase regulator activity / positive regulation of mismatch repair / positive regulation of myeloid progenitor 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 / regulation of T cell mediated immune response to tumor cell ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of mismatch repair / positive regulation of myeloid progenitor 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 / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / plasmacytoid dendritic cell activation / myeloid dendritic cell activation / glucose mediated signaling pathway / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / C-X-C chemokine binding / 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 amyloid precursor protein catabolic process / positive regulation of glycogen catabolic process / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / transcytosis / RAGE receptor binding / positive regulation of interleukin-1 production / eye development / Regulation of TLR by endogenous ligand / bubble DNA binding / induction of positive chemotaxis / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / myeloid cell differentiation / myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / regulation of nucleotide-excision repair / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / S100 protein binding / positive regulation of p38MAPK cascade / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / cellular response to interleukin-7 / regulation of long-term synaptic potentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / endothelial cell proliferation / negative regulation of connective tissue replacement involved in inflammatory response wound healing / glycogen catabolic process / apoptotic cell clearance / regulation of spontaneous synaptic transmission / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / dendritic cell chemotaxis / DNA binding, bending / IRAK4 deficiency (TLR2/4) / positive regulation of DNA binding / scavenger receptor activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / laminin receptor activity / positive regulation of double-strand break repair / negative regulation of interleukin-10 production / positive regulation of wound healing / phosphatidylserine binding / chemoattractant activity / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / negative regulation of type II interferon production / DNA topological change / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / protein kinase activator activity / positive regulation of blood vessel endothelial cell migration / Pyroptosis / phagocytosis / phagocytic cup / response to glucocorticoid / transport across blood-brain barrier / four-way junction DNA binding / positive regulation of chemokine production
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 ...: / 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 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35276.png

Downloads & links

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Map

FileDownload / File: emd_35276.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 200 pix.
= 393.4 Å		1.97 Å/pix.
x 200 pix.
= 393.4 Å		1.97 Å/pix.
x 200 pix.
= 393.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.967 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Additional map: #1

Fileemd_35276_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35276_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35276_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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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)

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