1b3t

EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX

Method: X-RAY DIFFRACTION Dmax: 67.8 Å Quality: EXCELLENT

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

PROTEIN (NUCLEAR PROTEIN EBNA1)

Human herpesvirus 4

UniProt Q69477

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 Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 23–169 Chain B; UniProt 23–169 Fragment:DNA-BINDING AND DIMERIZATION DOMAIN RESIDUES 459 - 607 ;DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3') ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;277 K;METHOD - HANGING DROP VAPOR DIFFUSION. RESERVOIR: 100 MM MES (PH 5.6) 20% PEG 4000, 500 MM NACL, 10 MM MGCL2, 10 MM DTT PROTEIN: 10MG/ML 1MM HEPES PH 7.2 1M NACL, 10 MM DTT DRY DNA RESUSPENDED IN THE PROTEIN CONTAINING SOLUTION IN MOLAR RATIO 1.5 (DSDNA) / 1.0 (EBNA1 DIMER) DROP: 50% PROTEIN/DNA SOLUTION 50% RESERVOIR SOLUTION CRYSTALLIZATION TEMPERATURE: 4 GEDREES C, vapor diffusion - hanging drop, temperature 277K Resolution 2.20 Å R-free 0.268

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q69477_9GAMA
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–147; UniProt 23–169 Author chain B; PDBConstruct 1–147; UniProt 23–169

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 1b3t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b3t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b3t
Deposition date deposition_date1998-12-14
Structure title titleEBNA-1 NUCLEAR PROTEIN/DNA COMPLEX
Keywords keywordsNUCLEAR PROTEIN, PROTEIN-DNA COMPLEX, DNA-BINDING, ACTIVATOR, ORIGIN-BINDING PROTEIN; PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.85
Radius of gyration Rg (electron density) rg_electron20.59
Forward intensity I(0) i041186900.00
Molecular weight molecular_weight43019.0 kDa
Excluded volume excluded_volume50921 ų
Envelope volume envelope_volume60139 ų
Hydration-shell volume shell_volume23952 ų
Envelope diameter envelope_diameter69.4
Shell Rg shell_rg27.67
Envelope Rg envelope_rg20.86
Shape Rg shape_rg20.54
Total Rg total_rg21.45
Total atoms total_atoms2982
Residues n_residues330
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.8
Rg (real space) rg_real21.71
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real4.1190e+07
I(0) uncertainty (real space) i0_real_error5.4710e+05
Rg (reciprocal space) rg_reciprocal21.74
I(0) (reciprocal space) i0_reciprocal41190000.0000
Solution quality estimate total_estimate0.9064
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.141
Kurtosis Kurtosis kurtosis-0.496
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5957000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b3ta_
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_idd1b3tb_
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_id1b3tA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id1b3tB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

8. Citations (3)

9. Files and Curves (10)