Download MendeleyVisualizing DNA polymerase iota catalyze Hoogsteen-directed DNA synthesis
Frevert, Z., Reusch, D.T., Gildenberg, M.S., Jordan, S.M., Ryan, B.J., Freudenthal, B.D., Washington, M.T.(2025) Nat Commun 16: 5979
9DDR | pdb_00009ddr
Ternary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP
- PDB DOI: https://doi.org/10.2210/pdb9DDR/pdb
- Classification: REPLICATION
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-08-28 Released: 2025-07-09
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.280 (Depositor), 0.280 (DCC)
- R-Value Work: 0.237 (Depositor), 0.237 (DCC)
- R-Value Observed: 0.239 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase iota | 420 | Homo sapiens | Mutation(s): 0 Gene Names: POLI, RAD30B EC: 2.7.7.7 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4 Go to UniProtKB: Q9UNA4 | |||||
PHAROS: Q9UNA4 GTEx: ENSG00000101751 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UNA4 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') | 18 | Homo sapiens |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TTP (Subject of Investigation/LOI) Query on TTP | C [auth A] | THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N |  | ||
| CA Query on CA | D [auth A], E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.280 (Depositor), 0.280 (DCC)
- R-Value Work: 0.237 (Depositor), 0.237 (DCC)
- R-Value Observed: 0.239 (Depositor)
Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 97.556 | α = 90 |
| b = 97.556 | β = 90 |
| c = 202.148 | γ = 120 |
| Software Name | Purpose |
|---|---|
| Coot | model building |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-07-09 Deposition Author(s): Frevert, Z., Reusch, D., Freudenthal, B., Washington, M.T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM081433 |
Revision History (Full details and data files)
- Version 1.0: 2025-07-09
Type: Initial release
