SAXSdb — 1gt0

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

OCTAMER-BINDING TRANSCRIPTION FACTOR 1

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 280–438	Fragment：POU DOMAIN RESIDUES 280-438 Mutation：YES	;5'-D(TPTPCPTPTPTPGPTPTPTP* GPGPAP* TPGPCPTPAPAPTPGPGPGPA)-3' ; × 1 ;5'-D(APTPCPCPCPAPTPTPAPGP* CPAPTPCPCPAPAPAPCPAPAPAPGP*A)-3' ; × 1 TRANSCRIPTION FACTOR SOX-2 × 1 （P48432）	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

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 1GT0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CQT CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT Deposited 1999-08-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 277–439（163 aa） Fragment：OCT-1 POU DOMAIN, RESIDUES 278-439	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.326
1CQT CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT Deposited 1999-08-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 277–439（163 aa） Fragment：OCT-1 POU DOMAIN, RESIDUES 278-439	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.326
1E3O Crystal structure of Oct-1 POU dimer bound to MORE Deposited 2000-06-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain C 280–438（159 aa） Fragment：DNA-BINDING DOMAIN	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；22% PEG3350, 50MM HEPES, PH 7.0, 1.8MM SPERMINE	Resolution 1.90 Å R-free 0.242
1HF0 Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer Deposited 2000-11-27	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 280–438（159 aa） Fragment：DNA-BINDING DOMAIN Chain B 280–438（159 aa） Fragment：DNA-BINDING DOMAIN	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；pH 5.30	Resolution 2.70 Å R-free 0.294
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 mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 303–465（163 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
1OCT CRYSTAL STRUCTURE OF THE OCT-1 POU DOMAIN BOUND TO AN OCTAMER SITE: DNA RECOGNITION WITH TETHERED DNA-BINDING MODULES Deposited 1994-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 284–439（156 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1POG SOLUTION STRUCTURE OF THE OCT-1 POU-HOMEO DOMAIN DETERMINED BY NMR AND RESTRAINED MOLECULAR DYNAMICS Deposited 1994-10-12	Different construct Different mutation/modification 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 378–437（60 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1POU THE SOLUTION STRUCTURE OF THE OCT-1 POU-SPECIFIC DOMAIN REVEALS A STRIKING SIMILARITY TO THE BACTERIOPHAGE LAMBDA REPRESSOR DNA-BINDING DOMAIN Deposited 1993-06-14	Different construct Different mutation/modification 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 284–354（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PO2F1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–159； UniProt 280–438

TRANSCRIPTION FACTOR SOX-2

MUS MUSCULUS

UniProt P48432

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	Fragment：HMG DOMAIN RESIDUES 41-120	;5'-D(TPTPCPTPTPTPGPTPTPTP* GPGPAP* TPGPCPTPAPAPTPGPGPGPA)-3' ; × 1 ;5'-D(APTPCPCPCPAPTPTPAPGP* CPAPTPCPCPAPAPAPCPAPAPAPGP*A)-3' ; × 1 OCTAMER-BINDING TRANSCRIPTION FACTOR 1 × 1 （P14859）	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

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 1GT0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HT5 Oct4/Sox2:UTF1 structure Deposited 2018-10-03	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）	Not recorded	No recorded non-water small molecule	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
8BX1 Oct4/Sox2 protein:DNA complex Deposited 2022-12-07	Different construct 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 construct 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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–80； UniProt 41–120

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	1gt0
Deposition date deposition_date	2002-01-09
Structure title title	Crystal structure of a POU/HMG/DNA ternary complex
Keywords keywords	TRANSCRIPTION FACTOR, POU FACTORS, SOX PROTEINS, 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	25.95 Å
Radius of gyration Rg (electron density) rg_electron	25.99 Å
Forward intensity I(0) i0	41362900.00
Molecular weight molecular_weight	39865.0 kDa
Excluded volume excluded_volume	45614 Å³
Envelope volume envelope_volume	63257 Å³
Hydration-shell volume shell_volume	21415 Å³
Envelope diameter envelope_diameter	90.4 Å
Shell Rg shell_rg	31.69 Å
Envelope Rg envelope_rg	25.94 Å
Shape Rg shape_rg	25.98 Å
Total Rg total_rg	26.56 Å
Total atoms total_atoms	2743
Residues n_residues	266
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	89.4 Å
Rg (real space) rg_real	26.14 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	4.1360e+07
I(0) uncertainty (real space) i0_real_error	5.6980e+05
Rg (reciprocal space) rg_reciprocal	26.09 Å
I(0) (reciprocal space) i0_reciprocal	41360000.0000
Solution quality estimate total_estimate	0.8420
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3925000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.694; Smooth: 0.951

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;5'-D(TPTPCPTPTPTPGPTPTPTP* GPGPAP* TPGPCPTPAPAPTPGPGPGPA)-3' ;
Molecular weight formula_weight	7436.8 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	2833

TTCTTTGTTTGGATGCTAATGGGA

Entity 2 Entity 2 polymer

Description description	;5'-D(APTPCPCPCPAPTPTPAPGP* CPAPTPCPCPAPAPAPCPAPAPAPGP*A)-3' ;
Molecular weight formula_weight	7299.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ATCCCATTAGCATCCAAACAAAGA

Entity 3 Entity 3 polymer

Description description	OCTAMER-BINDING TRANSCRIPTION FACTOR 1
Molecular weight formula_weight	18327.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRIN

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 4 Entity 4 polymer

Description description	TRANSCRIPTION FACTOR SOX-2
Molecular weight formula_weight	9833.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT

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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1gt0c1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.1 — Homeodomain

Domain ID domain_id	d1gt0c2
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.1 — POU-specific domain

Domain ID domain_id	d1gt0d_
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

CATH v4.4 (3 domains)

Domain ID domain_id	1gt0C01
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

Domain ID domain_id	1gt0C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1gt0D00
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	72.800 Å
Unit-cell length b length_b	72.800 Å
Unit-cell length c length_c	172.400 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2850

fit	/app/data/saxs_computation/gt/1gt0/1gt0.fit
pddf	/app/data/pr_computation/gt/1gt0/1gt0.pr.out
profile	/app/data/saxs_computation/gt/1gt0/1gt0.dat

Crystal structure of a POU/HMG/DNA ternary complex

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

OCTAMER-BINDING TRANSCRIPTION FACTOR 1

State in the Current Structure

Other States of the Same Protein in the Database

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

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

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)