8I9M: The RAGE and HMGB1 complex

The RAGE and HMGB1 complex. Determined by electron microscopy at 5.19 Å resolution. Released 14 Feb 2024.

Method: Electron microscopy
Resolution: 5.19 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,227
Mol. weight: 31.66 kDa
Released: 14 Feb 2024

Explore 8I9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I9M contains 3 α-helices and 8 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	91	1	1
β-strand	94	1	1
α-helix	122-125	4
α-helix	132-135	4

Chain B: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
β-strand	90	1	2
β-strand	97-98	2	3
β-strand	108-109	2	3
β-strand	113	1	2
β-strand	141	1	4
β-strand	175	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
High mobility group protein B1	A	protein	75	Homo sapiens	P09429 (AlphaFold model)
Advanced glycosylation end product-specific receptor	B	protein	211	Homo sapiens	Q15109 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8I9M_1 High mobility group protein B1 (chains A)
FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKA
AKLKEKYEKDIAAYR

Sequence of entity 2 (B), FASTA

>8I9M_2 Advanced glycosylation end product-specific receptor (chains B)
AQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNG
SLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQIPGKPEIVDSASELTAGVPNKVG
TCVSEGSYPAGTLSWHLDGKPLVPNEKGVSVKEQTRRHPETGLFTLQSELMVTPARGGDP
RPTFSCSFSPGLPRHRALRTAPIQPRVWEPV

Primary citation

The RAGE and HMGB1 complex. Han, C.W., Kim, H.J. To be published.

Other PDB entries of the same protein (UniProt P09429 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CG9 2.94 Å, Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2
6CIK 3.15 Å, Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+
6CG0 3.17 Å, Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)
6CIM 3.6 Å, Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+
6OEM 3.6 Å, Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0)
6OEO 3.69 Å, Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1)
6CIJ 3.9 Å, Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
6CIL 4.15 Å, Pre-reaction complex, RAG1(E962Q)/2-intact/intact 12/23RSS complex in MN2+
6OEN 4.3 Å, Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1)
2LY4 HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain…
2RTU Solution structure of oxidized human HMGB1 A box
2YRQ Solution structure of the tandem HMG box domain from Human High mobility group protein B1

Browse structure collections

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