SAXSdb — 2le4

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

Transcription factor SOX-2

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 39–118	Fragment：HMG box DNA binding residues 39-118	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.7；298 K；Ionic strength (raw mmCIF value) 100 mM；Pressure AMBIENT NMR sample composition：0.7 mM [U-100% 13C; U-100% 15N] Sox2, 7 % DTT, 95% H2O, 5% D2O \| 95% H2O/5% 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 2LE4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O4X TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT Deposited 2003-07-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 39–121（83 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 10 mM SODIUM PHOSPHATE	Resolution not provided
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21	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 36–121（86 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.	Resolution 5.10 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric	Chain L 37–118（82 aa）	Not recorded	PTD PENTANEDIAL × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
6WX7 SOX2 bound to Importin-alpha 2 Deposited 2020-05-09	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 B 39–127（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；750mM sodium citrate (pH7), 10 mM DTT	Resolution 2.70 Å R-free 0.227
6WX8 SOX2 bound to Importin-alpha 3 Deposited 2020-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 39–127（89 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.2M (NH4)2SO4, 0.1M HEPES pH 6.5	Resolution 2.30 Å R-free 0.245
6WX8 SOX2 bound to Importin-alpha 3 Deposited 2020-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 39–127（89 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.2M (NH4)2SO4, 0.1M HEPES pH 6.5	Resolution 2.30 Å R-free 0.245
6WX9 SOX2 bound to Importin-alpha 5 Deposited 2020-05-10	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 B 39–127（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2M sodium/potassium phosphate, 20% (w/v) PEG3350	Resolution 2.80 Å R-free 0.251
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric	Chain L 37–118（82 aa）	Not recorded	PTD PENTANEDIAL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.42 Å
9QPF Solution structure of Sox2 DBD Deposited 2025-03-27	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–127（95 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；293 K；Ionic strength (raw mmCIF value) 150；Pressure AMBIENT NMR sample composition 0.25 mM [U-13C; U-15N] Sox2-DBD, 135 mM potassium chloride, 20 mM TRIS, 15 mM sodium chloride, 0.01 % v/v sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.25 mM [U-13C; U-15N] Sox2-DBD, 135 mM potassium chloride, 20 mM TRIS, 15 mM sodium chloride, 0.01 % v/v sodium azide, 5 % v/v pentaethylene glycol monodecyl/n-Hexanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain W 37–118（82 aa）	Not recorded	PTD PENTANEDIAL × 16 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain W 37–118（82 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric	Chain W 37–118（82 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric	Chain W 37–118（82 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SOX2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–81； UniProt 39–118

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	2le4
Deposition date deposition_date	2011-06-06
Structure title title	Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
Keywords keywords	Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, TRANSCRIPTION, CESG; TRANSCRIPTION
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	16.17 Å
Radius of gyration Rg (electron density) rg_electron	16.28 Å
Forward intensity I(0) i0	602074000.00
Molecular weight molecular_weight	198150.0 kDa
Excluded volume excluded_volume	245930 Å³
Envelope volume envelope_volume	57176 Å³
Hydration-shell volume shell_volume	21733 Å³
Envelope diameter envelope_diameter	77.0 Å
Shell Rg shell_rg	29.08 Å
Envelope Rg envelope_rg	24.03 Å
Shape Rg shape_rg	16.25 Å
Total Rg total_rg	16.79 Å
Total atoms total_atoms	28300
Residues n_residues	1620
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	43.3 Å
Rg (real space) rg_real	14.98 Å
Rg uncertainty (real space) rg_real_error	0.08 Å
I(0) (real space) i0_real	5.7240e+08
I(0) uncertainty (real space) i0_real_error	4.8270e+06
Rg (reciprocal space) rg_reciprocal	16.41 Å
I(0) (reciprocal space) i0_reciprocal	602100000.0000
Solution quality estimate total_estimate	0.6871
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.355
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	3.1120
Highest regularization parameter α highest_alpha	206700.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.988; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2le4a1
Class class	a — All alpha proteins
Fold Fold fold	a.21 — HMG-box
Superfamily Superfamily superfamily	a.21.1 — HMG-box
Family Family family	a.21.1.1 — HMG-box

Domain ID domain_id	d2le4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2le4A00
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	Transcription factor SOX-2
Molecular weight formula_weight	9920.6 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	28300

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/le/2le4/2le4.fit
pddf	/app/data/pr_computation/le/2le4/2le4.pr.out
profile	/app/data/saxs_computation/le/2le4/2le4.dat

Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2

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

Transcription factor SOX-2

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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)