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2v6z

Solution Structure of Amino-Terminal Domain of Human DNA Polymerase Epsilon Subunit B

Method: SOLUTION NMR Dmax: 38.2 Å Quality: GOOD
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain M； UniProt 1–75 Fragment：AMINO TERMINAL DOMAIN, RESIDUES 1-75 Mutation：YES No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.62；298 K；Pressure 1.0 NMR sample composition：0.7 MM PROTEIN NMR sample composition：155 MM NACL NMR sample composition：25 MM TRIS-HCL NMR sample composition：25 MM IMIDAZOLE NMR sample composition：1.25 MM EDTA NMR sample composition：93% H2O, 7% D2O 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 2V6Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5VBN Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2017-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–527（527 aa）
Not recorded 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
5VBN Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit Deposited 2017-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–527（527 aa）
Not recorded 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
7PFO Core human replisome Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain A 1–527（527 aa）
Not recorded ZN ZINC ION × 5 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7PLO H. sapiens replisome-CUL2/LRR1 complex Deposited 2021-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 1–527（527 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

3 other PDB entries and 4 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 M； PDBConstruct 25–99； UniProt 1–75

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 2v6z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2v6z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2v6z
Deposition date deposition_date2007-07-24
Structure title titleSolution Structure of Amino-Terminal Domain of Human DNA Polymerase Epsilon Subunit B
Keywords keywordsDNA REPLICATION, DNA POLYMERASE EPSILON, DPOE2, TRANSFERASE, AAA PROTEIN FAMILY; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.31 Å
Radius of gyration Rg (electron density) rg_electron11.84 Å
Forward intensity I(0) i0385347000.00
Molecular weight molecular_weight167950.0 kDa
Excluded volume excluded_volume211920 ų
Envelope volume envelope_volume19486 ų
Hydration-shell volume shell_volume12073 ų
Envelope diameter envelope_diameter44.3 Å
Shell Rg shell_rg19.51 Å
Envelope Rg envelope_rg14.13 Å
Shape Rg shape_rg11.80 Å
Total Rg total_rg12.16 Å
Total atoms total_atoms22020
Residues n_residues1500
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 dmax38.2 Å
Rg (real space) rg_real12.21 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real3.8530e+08
I(0) uncertainty (real space) i0_real_error4.2810e+06
Rg (reciprocal space) rg_reciprocal12.22 Å
I(0) (reciprocal space) i0_reciprocal385300000.0000
Solution quality estimate total_estimate0.7873
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.4 Å
Skewness Skewness skewness0.051
Kurtosis Kurtosis kurtosis-0.162
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha291900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.757; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2v6zM00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)