SAXSdb — 6ht5

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

Transcription factor SOX-2

Mus musculus

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain D； UniProt 41–120	Not recorded	;DNA (5'-D(PCPCPTPCPAPTPTPGPTPTPAPTPGPCPTPAPGPTPGPAPAPG)-3') ; × 1 ;DNA (5'-D(TPTPCPAPCPTPAPGPCPAPTPAPAPCPAPAPTPGPAPGP*G)-3') ; × 1 POU domain, class 5, transcription factor 1 × 1 （P20263）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；100 mM 4-morpholineethanesulfonic acid at pH 6.0, 33% v/v 2-methyl-2,4-pentanediol	Resolution 3.45 Å R-free 0.248

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 6HT5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GT0 Crystal structure of a POU/HMG/DNA ternary complex Deposited 2002-01-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 41–120（80 aa） Fragment：HMG DOMAIN RESIDUES 41-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；18% PEG3350, 50 MM HEPES PH 7.0, 20 MM MGCL2, 5% GLYCEROL	Resolution 2.60 Å R-free 0.285
8BX1 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 41–120（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M sodium acetate, 12% (v/v) PEG 4000	Resolution 2.50 Å R-free 0.274
8BX2 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 41–120（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES, 70% (v/v) MPD	Resolution 3.14 Å R-free 0.252

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SOX2_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 4–83； UniProt 41–120

POU domain, class 5, transcription factor 1

Mus musculus

UniProt P20263

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–DNA Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain E； UniProt 131–282	Not recorded	;DNA (5'-D(PCPCPTPCPAPTPTPGPTPTPAPTPGPCPTPAPGPTPGPAPAPG)-3') ; × 1 ;DNA (5'-D(TPTPCPAPCPTPAPGPCPAPTPAPAPCPAPAPTPGPAPGP*G)-3') ; × 1 Transcription factor SOX-2 × 1 （P48432）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；100 mM 4-morpholineethanesulfonic acid at pH 6.0, 33% v/v 2-methyl-2,4-pentanediol	Resolution 3.45 Å R-free 0.248

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 6HT5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OCP SOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN Deposited 1995-02-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 217–282（66 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
3L1P POU protein:DNA complex Deposited 2009-12-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 131–282（152 aa） Fragment：UNP residues 131-282 Chain B 131–282（152 aa） Fragment：UNP residues 131-282	Mutation：C48S, C61S, C84S, C115S, C142S Mutation：C48S, C61S, C84S, C115S, C142S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.257
8BX1 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 131–282（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M sodium acetate, 12% (v/v) PEG 4000	Resolution 2.50 Å R-free 0.274
8BX2 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 131–282（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES, 70% (v/v) MPD	Resolution 3.14 Å R-free 0.252

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PO5F1_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 3–154； UniProt 131–282

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	6ht5
Deposition date deposition_date	2018-10-03
Structure title title	Oct4/Sox2:UTF1 structure
Keywords keywords	Cell reprogramming, transcription factor, DNA binding, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.63 Å
Radius of gyration Rg (electron density) rg_electron	22.90 Å
Forward intensity I(0) i0	30320900.00
Molecular weight molecular_weight	33288.0 kDa
Excluded volume excluded_volume	37853 Å³
Envelope volume envelope_volume	53332 Å³
Hydration-shell volume shell_volume	20619 Å³
Envelope diameter envelope_diameter	94.0 Å
Shell Rg shell_rg	28.22 Å
Envelope Rg envelope_rg	23.47 Å
Shape Rg shape_rg	22.86 Å
Total Rg total_rg	23.58 Å
Total atoms total_atoms	2287
Residues n_residues	220
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	87.9 Å
Rg (real space) rg_real	23.74 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	3.0320e+07
I(0) uncertainty (real space) i0_real_error	5.1390e+05
Rg (reciprocal space) rg_reciprocal	23.72 Å
I(0) (reciprocal space) i0_reciprocal	30320000.0000
Solution quality estimate total_estimate	0.8215
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.462
Kurtosis Kurtosis kurtosis	-0.174
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3589000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.684; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PCPCPTPCPAPTPTPGPTPTPAPTPGPCPTPAPGPTPGPAPAPG)-3') ;
Molecular weight formula_weight	6757.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	2287

CCTCATTGTTATGCTAGTGAAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPTPCPAPCPTPAPGPCPAPTPAPAPCPAPAPTPGPAPGP*G)-3') ;
Molecular weight formula_weight	6455.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

TTCACTAGCATAACAATGAGG

Entity 3 Entity 3 polymer

Description description	Transcription factor SOX-2
Molecular weight formula_weight	10092.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GAMDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	POU domain, class 5, transcription factor 1
Molecular weight formula_weight	17831.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GADMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6ht5D00
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	6ht5E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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8. Citations (1)

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Unit-cell length a length_a	165.170 Å
Unit-cell length b length_b	165.170 Å
Unit-cell length c length_c	39.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.451 Å
Low-resolution limit resolution_low	47.680 Å
R factor r_factor	0.2050
R_work r_work	0.2011
R_free r_free	0.2484

fit	/app/data/saxs_computation/ht/6ht5/6ht5.fit
pddf	/app/data/pr_computation/ht/6ht5/6ht5.pr.out
profile	/app/data/saxs_computation/ht/6ht5/6ht5.dat

Oct4/Sox2:UTF1 structure

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

POU domain, class 5, transcription factor 1

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 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)