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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P09429 New Search
13PDB entries
13Biological assembly
15chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2LY4 HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail Deposited 2012-09-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 2–84（83 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RTU Solution structure of oxidized human HMGB1 A box Deposited 2013-09-12 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–84（84 aa） Fragment：HMG box 1, UNP residues 1-84
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；293 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition 0.5-0.6 mM [U-13C; U-15N] protein-1, 50 mM potassium phosphate-2, 10 % [U-2H] D2O-3, 150 mM potassium chloride-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5-0.6 mM [U-13C; U-15N] protein-5, 5 % C12E5/n-hexanol-6, 10 % U-2H D2O-7, 150 mM potassium chloride-8, 50 mM potassium phosphate-9, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2YRQ Solution structure of the tandem HMG box domain from Human High mobility group protein B1 Deposited 2007-04-02 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–166（166 aa） Fragment：HMG box domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.09mM HMG box domain U-15N,13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
6CG0 Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A) Deposited 2018-02-19 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric（11） Consistent with all polymers
Chain N 15–140（126 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
6CIJ Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) Deposited 2018-02-24 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric（11） Consistent with all polymers
Chain N 1–163（163 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6CIK Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ Deposited 2018-02-24 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric（10） Consistent with all polymers
Chain N 1–163（163 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；12-16% PEG 3350, 200 mM NaNO3, 50 mM HEPES, pH 6.9
Resolution 3.15 Å R-free 0.249
6CIL PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+ Deposited 2018-02-24 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric（9） Consistent with all polymers
Chain N 1–163（163 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 4.15 Å R-free 0.231
6CIM Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+ Deposited 2018-02-24 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric（10） Consistent with all polymers
Chain N 1–163（163 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 3.60 Å R-free 0.254
6OEM Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) Deposited 2019-03-27 Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric（10） Consistent with all polymers
Chain H 15–155（141 aa）
Chain N 15–155（141 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6OEN Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1) Deposited 2019-03-27 Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric（10） Consistent with all polymers
Chain H 1–163（163 aa）
Chain N 1–163（163 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OEO Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) Deposited 2019-03-27 Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric（9） Consistent with all polymers
Chain N 1–163（163 aa）
Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
8I9M The RAGE and HMGB1 complex Deposited 2023-02-07 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 89–163（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.19 Å
9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain K 1–215（215 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied to grid.
Resolution 2.94 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.