SAXSdb — 2yrq

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1. Protein Identity and Related Structures Protein Identity & Related Structures

High mobility group protein B1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–166	Fragment：HMG box domain	No other associated polymer	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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2YRQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and 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	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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
6CG0 Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A) Deposited 2018-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric	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	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	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	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	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

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HMGB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–173； UniProt 1–166

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2yrq
Deposition date deposition_date	2007-04-02
Structure title title	Solution structure of the tandem HMG box domain from Human High mobility group protein B1
Keywords keywords	;HMG box domain, DNA binding, Helix-turn-helix motif, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.93 Å
Radius of gyration Rg (electron density) rg_electron	23.68 Å
Forward intensity I(0) i0	2192800000.00
Molecular weight molecular_weight	392610.0 kDa
Excluded volume excluded_volume	491240 Å³
Envelope volume envelope_volume	149800 Å³
Hydration-shell volume shell_volume	42635 Å³
Envelope diameter envelope_diameter	109.6 Å
Shell Rg shell_rg	36.89 Å
Envelope Rg envelope_rg	28.74 Å
Shape Rg shape_rg	23.67 Å
Total Rg total_rg	24.09 Å
Total atoms total_atoms	55400
Residues n_residues	3460
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	96.1 Å
Rg (real space) rg_real	24.03 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	2.1930e+09
I(0) uncertainty (real space) i0_real_error	3.3510e+07
Rg (reciprocal space) rg_reciprocal	24.01 Å
I(0) (reciprocal space) i0_reciprocal	2193000000.0000
Solution quality estimate total_estimate	0.7694
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.516
Kurtosis Kurtosis kurtosis	0.056
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	20980000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.477; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.568; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2yrqA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

Domain ID domain_id	2yrqA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	10 — High mobility group box domain

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8. Citations (1)

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Description description	High mobility group protein B1
Molecular weight formula_weight	19674.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	55400

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/yr/2yrq/2yrq.fit
pddf	/app/data/pr_computation/yr/2yrq/2yrq.pr.out
profile	/app/data/saxs_computation/yr/2yrq/2yrq.dat

Solution structure of the tandem HMG box domain from Human High mobility group protein B1

1. Protein Identity and Related Structures Protein Identity & Related Structures

High mobility group protein B1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)