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1t6l

Crystal Structure of the Human Cytomegalovirus DNA Polymerase Subunit, UL44

Method: X-RAY DIFFRACTION Dmax: 68.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase processivity factor

Human herpesvirus 5

UniProt P16790

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 1–290 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；polyethylene glycol 4000, sodium acetate, sodium chloride, dithiothreitol , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 1.85 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.

Other PDB Difference from Current Entry 1T6L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YYP Crystal structure of cytomegalovirus UL44 bound to C-terminal peptide from CMV UL54 Deposited 2005-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–290（290 aa） Fragment：N-TERMINAL DOMAIN
Not recorded SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；295 K；2 M ammonium sulfate, 100 mM phosphate-citrate, and 10 mM DTT , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.227
5IWD HCMV DNA polymerase subunit UL44 complex with a small molecule Deposited 2016-03-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–290（290 aa）
Not recorded 6EV 5-methylidene-3-(methylsulfanyl)-2-benzothiophen-4(5H)-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；1 uL of 10 mg/mL UL44 in the storage buffer (20 mM Tris (pH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 1 uL crystallization buffer (75 mM ammonium sulfate, 50 mM HEPES (pH 7.5) and 10% PEG4K) were mixed in hanging drops. Crystals were obtained by vapor diffusion over a 1.8 M NaCl solution, after one day
Resolution 2.56 Å R-free 0.267
5IXA HCMV DNA polymerase processivity subunit UL44 at neutral pH and low salt Deposited 2016-03-23 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–290（290 aa）
Chain B 1–290（290 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.2 microliter of 8 mg/mL UL44 in the storage buffer (20 mM Tris (PH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 0.2 microliter crystallization buffer (0.1 M HEPES (PH 7.0) and 18% PEG12K) were mixed and crystallized in sitting drops over the crystallization buffer at room temperature
Resolution 2.68 Å R-free 0.259
8QXW HCMV DNA polymerase processivity factor UL44 unphosphorylated NLS 410-433 bound to mouse importin alpha 2 Deposited 2023-10-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 410–433（24 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Sodium citrate 0.65M, HEPES pH7.5, DTT 0.01M
Resolution 2.00 Å R-free 0.221
8QXX HCMV DNA polymerase processivity factor UL44 phosphorylated NLS 410-433 bound to mouse importin alpha 2 Deposited 2023-10-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 410–433（24 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；Sodium citrate 0.65M, HEPES pH7.0, DTT 0.01M
Resolution 1.90 Å R-free 0.204

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VPAP_HCMVA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–290； UniProt 1–290

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 1t6l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t6l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t6l
Deposition date deposition_date2004-05-06
Structure title titleCrystal Structure of the Human Cytomegalovirus DNA Polymerase Subunit, UL44
Keywords keywordsProcessivity Fold, REPLICATION; REPLICATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.65 Å
Radius of gyration Rg (electron density) rg_electron19.68 Å
Forward intensity I(0) i012825600.00
Molecular weight molecular_weight27620.0 kDa
Excluded volume excluded_volume34968 ų
Envelope volume envelope_volume41391 ų
Hydration-shell volume shell_volume18168 ų
Envelope diameter envelope_diameter69.5 Å
Shell Rg shell_rg25.36 Å
Envelope Rg envelope_rg19.88 Å
Shape Rg shape_rg19.70 Å
Total Rg total_rg20.50 Å
Total atoms total_atoms1941
Residues n_residues249
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 dmax68.6 Å
Rg (real space) rg_real20.67 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real1.2830e+07
I(0) uncertainty (real space) i0_real_error1.7970e+05
Rg (reciprocal space) rg_reciprocal20.67 Å
I(0) (reciprocal space) i0_reciprocal12830000.0000
Solution quality estimate total_estimate0.7941
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.9 Å
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.333
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4982000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; 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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1t6la1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.2 — DNA polymerase processivity factor
Domain ID domain_idd1t6la2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (1 domains)

Domain ID domain_id1t6lA00
Class class3 — Alpha Beta
Architecture architecture70 — Box
Topology topology10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)