SAXSdb — 6t78

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

Transcription factor SOX-11

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 33–138	Not recorded	;DNA (5'-D(TPAPTPTPGPTPTPTPAPTPTPTPTPGPTPT)-3') ; × 1 ;DNA (5'-D(APAPCPAPAPAPAPTPAPAPAPCPAPAPTPA)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；Sodium Acetate 100 mM pH 4.5, Calcium Acetate Hydrate 200 mM, 15-18 % PEG 400	Resolution 2.50 Å R-free 0.258
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 33–138	Not recorded	;DNA (5'-D(TPAPTPTPGPTPTPTPAPTPTPTPTPGPTPT)-3') ; × 1 ;DNA (5'-D(APAPCPAPAPAPAPTPAPAPAPCPAPAPTPA)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；Sodium Acetate 100 mM pH 4.5, Calcium Acetate Hydrate 200 mM, 15-18 % PEG 400	Resolution 2.50 Å R-free 0.258

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 6T78	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21	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 33–138（106 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 3.70 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 33–138（106 aa） Chain L 33–138（106 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 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21	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 33–138（106 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 4.40 Å

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

View Construct and Data Evidence

UniProt name	SOX11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–109； UniProt 33–138 Author chain B； PDBConstruct 4–109； UniProt 33–138

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	6t78
Deposition date deposition_date	2019-10-21
Structure title title	Structure of human Sox11 transcription factor in complex with a short DNA fragment
Keywords keywords	Sox11, transcription factor, pioneer factor, DNA, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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	23.25 Å
Radius of gyration Rg (electron density) rg_electron	22.64 Å
Forward intensity I(0) i0	31917200.00
Molecular weight molecular_weight	34015.0 kDa
Excluded volume excluded_volume	38525 Å³
Envelope volume envelope_volume	52508 Å³
Hydration-shell volume shell_volume	20345 Å³
Envelope diameter envelope_diameter	81.0 Å
Shell Rg shell_rg	28.33 Å
Envelope Rg envelope_rg	22.79 Å
Shape Rg shape_rg	22.59 Å
Total Rg total_rg	23.36 Å
Total atoms total_atoms	2326
Residues n_residues	201
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	78.7 Å
Rg (real space) rg_real	23.30 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	3.1920e+07
I(0) uncertainty (real space) i0_real_error	4.2390e+05
Rg (reciprocal space) rg_reciprocal	23.29 Å
I(0) (reciprocal space) i0_reciprocal	31920000.0000
Solution quality estimate total_estimate	0.8830
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.373
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3623000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.971

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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	Transcription factor SOX-11
Molecular weight formula_weight	12856.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2332

SNAALDESDPDWCKTASGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLGKRWKMLKDSEKIPFIREAERLRLKHMADYPDYKYRPRKKPKMDPSAKPSASQSP

来源 Source

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPAPTPTPGPTPTPTPAPTPTPTPTPGPTPT)-3') ;
Molecular weight formula_weight	4890.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F

TATTGTTTATTTTGTT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APAPCPAPAPAPAPTPAPAPAPCPAPAPTPA)-3') ;
Molecular weight formula_weight	4900.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,G

AACAAAATAAACAATA

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6t78A00
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	6t78B00
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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Unit-cell length a length_a	106.130 Å
Unit-cell length b length_b	106.130 Å
Unit-cell length c length_c	76.890 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.504 Å
Low-resolution limit resolution_low	45.956 Å
R factor r_factor	0.2284
R_work r_work	0.2269
R_free r_free	0.2578

fit	/app/data/saxs_computation/t7/6t78/6t78.fit
pddf	/app/data/pr_computation/t7/6t78/6t78.pr.out
profile	/app/data/saxs_computation/t7/6t78/6t78.dat

Structure of human Sox11 transcription factor in complex with a short DNA fragment

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

Transcription factor SOX-11

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)