5vbn

Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit

Method: X-RAY DIFFRACTION Dmax: 124.0 Å Quality: GOOD

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

DNA polymerase epsilon subunit 2

Homo sapiens

UniProt P56282

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–527 Not recorded DNA polymerase epsilon catalytic subunit A × 1 (Q07864) SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP Resolution 2.35 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–527 Not recorded DNA polymerase epsilon catalytic subunit A × 1 (Q07864) SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP Resolution 2.35 Å R-free 0.264

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.

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

View Construct and Data Evidence
UniProt name DPOE2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–527; UniProt 1–527 Author chain E; PDBConstruct 1–527; UniProt 1–527

DNA polymerase epsilon catalytic subunit A

Homo sapiens

UniProt Q07864

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2142–2286 Fragment:UNP residues 2142-2286 DNA polymerase epsilon subunit 2 × 1 (P56282) SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP Resolution 2.35 Å R-free 0.264
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 2142–2286 Fragment:UNP residues 2142-2286 DNA polymerase epsilon subunit 2 × 1 (P56282) SO4 SULFATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;295 K;50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP Resolution 2.35 Å R-free 0.264

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.

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOE1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–145; UniProt 2142–2286 Author chain F; PDBConstruct 1–145; UniProt 2142–2286

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 5vbn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vbn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vbn
Deposition date deposition_date2017-03-29
Structure title titleCrystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit
Keywords keywordsreplication, DNA replication, polymerase, DNA polymerase, DNA polymerase epsilon, B-subunit, catalytic subunit, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.43
Radius of gyration Rg (electron density) rg_electron37.74
Forward intensity I(0) i0228160000.00
Molecular weight molecular_weight125930.0 kDa
Excluded volume excluded_volume158540 ų
Envelope volume envelope_volume203930 ų
Hydration-shell volume shell_volume44474 ų
Envelope diameter envelope_diameter123.2
Shell Rg shell_rg44.15
Envelope Rg envelope_rg37.62
Shape Rg shape_rg37.67
Total Rg total_rg38.37
Total atoms total_atoms8846
Residues n_residues1104
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 dmax124.0
Rg (real space) rg_real38.49
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real2.2820e+08
I(0) uncertainty (real space) i0_real_error4.3060e+06
Rg (reciprocal space) rg_reciprocal38.46
I(0) (reciprocal space) i0_reciprocal228200000.0000
Solution quality estimate total_estimate0.8854
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.655
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42090000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.742

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)