2RTU: Oxidized human HMGB1 A box

Solution structure of oxidized human HMGB1 A box. Determined by solution NMR. Released 5 Mar 2014.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 706
Mol. weight: 10.12 kDa
Released: 5 Mar 2014

Explore 2RTU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RTU contains 5 α-helices and 0 β-strands across 1 chain. 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	18-33	16
α-helix	41-52	12
α-helix	57-69	13
α-helix	71-78	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
High mobility group protein B1	A	protein	87	Homo sapiens	P09429 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2RTU_1 High mobility group protein B1 (chains A)
GSHMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK
GKFEDMAKADKARYEREMKTYIPPKGE

Primary citation

Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA. Wang, J., Tochio, N., Takeuchi, A. et al. Biochem Biophys Res Commun (2013) 441:701-706. PubMed

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)
8I9M 5.19 Å, The RAGE and HMGB1 complex
2LY4 HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain…
2YRQ Solution structure of the tandem HMG box domain from Human High mobility group protein B1

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