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1r8p

HPV-16 E2C solution structure

Method: SOLUTION NMR Dmax: 62.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulatory protein E2

Human papillomavirus type 16

UniProt P03120

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 286–365 Chain B； UniProt 286–365 Fragment：DNA binding domain No other associated polymer 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

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 1R8P 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 mutation/modification Different experimental method 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
1DTO CRYSTAL STRUCTURE OF THE COMPLETE TRANSACTIVATION DOMAIN OF E2 PROTEIN FROM THE HUMAN PAPILLOMAVIRUS TYPE 16 Deposited 2000-01-13 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 1–201（201 aa） Fragment：TRANSACTIVATION DOMAIN
Not recorded No recorded non-water small molecule 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
1ZZF The DNA-bound solution structure of HPV-16 E2 DNA-binding domain Deposited 2005-06-14 Different construct Different experimental conditions 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different ligand/ion Different experimental method 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 method 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 2–81； UniProt 286–365 Author chain B； PDBConstruct 2–81； UniProt 286–365

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1r8p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1r8p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1r8p
Deposition date deposition_date2003-10-28
Structure title titleHPV-16 E2C solution structure
Keywords keywordsdimeric beta-barrel, DNA binding protein, transcription factor, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.47 Å
Radius of gyration Rg (electron density) rg_electron17.25 Å
Forward intensity I(0) i01838390000.00
Molecular weight molecular_weight375600.0 kDa
Excluded volume excluded_volume475150 ų
Envelope volume envelope_volume68473 ų
Hydration-shell volume shell_volume25831 ų
Envelope diameter envelope_diameter72.1 Å
Shell Rg shell_rg29.24 Å
Envelope Rg envelope_rg22.23 Å
Shape Rg shape_rg17.21 Å
Total Rg total_rg17.62 Å
Total atoms total_atoms53279
Residues n_residues3240
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.1 Å
Rg (real space) rg_real17.42 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real1.8380e+09
I(0) uncertainty (real space) i0_real_error2.3970e+07
Rg (reciprocal space) rg_reciprocal17.43 Å
I(0) (reciprocal space) i0_reciprocal1838000000.0000
Solution quality estimate total_estimate0.8393
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.7 Å
Skewness Skewness skewness0.294
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.4550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1056000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.652; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.996
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1r8pa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.8 — Viral DNA-binding domain
Family Family familyd.58.8.1 — Viral DNA-binding domain
Domain ID domain_idd1r8pb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.8 — Viral DNA-binding domain
Family Family familyd.58.8.1 — Viral DNA-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id1r8pA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id1r8pB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
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8. Citations (1)

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9. Files and Curves (10)