SAXSdb — 1dto

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

REGULATORY PROTEIN E2

Human papillomavirus type 16

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–201	Fragment：TRANSACTIVATION DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；291 K；monomethylether PEG 5000, NaCl, isopropanol, triethanolamine,Tris-HCl, DTT, EDTA, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 1.90 Å R-free 0.305

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 1DTO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BY9 CRYSTAL STRUCTURE OF THE E2 DNA-BINDING DOMAIN FROM HUMAN PAPILLOMAVIRUS TYPE-16: IMPLICATIONS FOR ITS DNA BINDING-SITE SELECTION MECHANISM Deposited 1998-10-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 285–365（81 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；pH 6.2	Resolution 2.20 Å R-free 0.220
1R8P HPV-16 E2C solution structure Deposited 2003-10-28	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 286–365（80 aa） Fragment：DNA binding domain Chain B 286–365（80 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 50mM Phosphate；Pressure ambient NMR sample composition 1.8mM 15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT \| 95% H2O/5% D2O NMR sample composition 0.9mM 13C,15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT \| 95% H2O/5% D2O NMR sample composition 0.2mM 15N-labeled HPV-16 E2C, 50mM Sodium Phosphate, 5mM DTT \| 6% polyacrylamide gel	Resolution not provided
1ZZF The DNA-bound solution structure of HPV-16 E2 DNA-binding domain Deposited 2005-06-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 286–365（80 aa） Fragment：DNA-binding domain Chain B 286–365（80 aa） Fragment：DNA-binding domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；318 K；Ionic strength (raw mmCIF value) 250 mM NaCl；Pressure ambient NMR sample composition DNA-E2C complex (15N) 0.6mM, 25mM Acetate+ 10mM Phosphate, pH 5.6, NaCl 250mM, DTT 5mM \| 95% H20, 5% D2O NMR sample composition DNA-E2C complex (15N, 13C) 0.6mM, 25mM Acetate+ 10mM Phosphate, pH 5.6, NaCl 250mM, DTT 5mM \| 95% H20, 5% D2O NMR sample composition DNA-E2C complex (15N) 0.2mM, 25mM Acetate+ 10mM Phosphate, pH 5.6, NaCl 250mM, DTT 5mM, Philamentosus phage 17mg/ml \| 95% H20, 5% D2O	Resolution not provided
2NNU Crystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4 Deposited 2006-10-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–201（201 aa） Fragment：Activation Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100mM citrate, 1.8-2.0M Na-acetate, 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.59 Å R-free 0.233
2NNU Crystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4 Deposited 2006-10-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–201（201 aa） Fragment：Activation Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100mM citrate, 1.8-2.0M Na-acetate, 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.59 Å R-free 0.233
2Q79 Crystal Structure of single chain E2C from HPV16 with a 12aa linker for monomerization. Deposited 2007-06-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 285–365（81 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.21；298 K；80 mM sodium citrate, 1.53 M (NH4)2SO4, 150 mM sodium and potassium tartrate, pH 5.21, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.241
3MI7 An Enhanced Repressor of Human Papillomavirus E2 Protein Deposited 2010-04-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 283–365（83 aa） Fragment：UNP residues 283-365	Mutation：H290E, C309S	EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；100 mM sodium citrate, 100 mM ammonium acetate, 10% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	VE2_HPV16
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–221； UniProt 1–201

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	1dto
Deposition date deposition_date	2000-01-13
Structure title title	CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PROTEIN FROM THE HUMAN PAPILLOMAVIRUS TYPE 16
Keywords keywords	three-helix bundle, beta-sheet, Viral protein; VIRAL 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	22.39 Å
Radius of gyration Rg (electron density) rg_electron	21.65 Å
Forward intensity I(0) i0	9853020.00
Molecular weight molecular_weight	23412.0 kDa
Excluded volume excluded_volume	29219 Å³
Envelope volume envelope_volume	36821 Å³
Hydration-shell volume shell_volume	15383 Å³
Envelope diameter envelope_diameter	82.6 Å
Shell Rg shell_rg	26.80 Å
Envelope Rg envelope_rg	22.08 Å
Shape Rg shape_rg	21.60 Å
Total Rg total_rg	22.53 Å
Total atoms total_atoms	1650
Residues n_residues	200
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	77.8 Å
Rg (real space) rg_real	22.54 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	9.8530e+06
I(0) uncertainty (real space) i0_real_error	1.3970e+05
Rg (reciprocal space) rg_reciprocal	22.50 Å
I(0) (reciprocal space) i0_reciprocal	9853000.0000
Solution quality estimate total_estimate	0.7513
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2368000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.695; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dtoa1
Class class	b — All beta proteins
Fold Fold fold	b.91 — E2 regulatory, transactivation domain
Superfamily Superfamily superfamily	b.91.1 — E2 regulatory, transactivation domain
Family Family family	b.91.1.1 — E2 regulatory, transactivation domain

Domain ID domain_id	d1dtoa2
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 (2 domains)

Domain ID domain_id	1dtoA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	30 — E2 (early) protein, N terminal domain, subdomain 1

Domain ID domain_id	1dtoA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	200 — Regulatory Protein E2; Chain: A; Domain 2
Homologous superfamily homologous superfamily	10 — Papillomavirus E2 early protein domain

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8. Citations (2)

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Unit-cell length a length_a	54.680 Å
Unit-cell length b length_b	54.680 Å
Unit-cell length c length_c	155.730 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	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2360
R_work r_work	0.2320
R_free r_free	0.3050

Description description	REGULATORY PROTEIN E2
Molecular weight formula_weight	25699.0 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	1861

CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PROTEIN FROM THE HUMAN PAPILLOMAVIRUS TYPE 16

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

REGULATORY PROTEIN E2

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Human papillomavirus type 16
NCBI Class编号 ncbi_taxonomy_id	333760
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

fit	/app/data/saxs_computation/dt/1dto/1dto.fit
pddf	/app/data/pr_computation/dt/1dto/1dto.pr.out
profile	/app/data/saxs_computation/dt/1dto/1dto.dat