8V7B

Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

PDB DOI: https://doi.org/10.2210/pdb8V7B/pdb
NAKB: 8V7B

Classification: Transferase/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-04 Released: 2024-05-15
Deposition Author(s): Chang, C., Gao, Y.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

Chang, C., Gao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 55.55 kDa
Atom Count: 4,268
Modelled Residue Count: 450
Deposited Residue Count: 455
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	435	Homo sapiens	Mutation(s): 0 Gene Names: POLH, RAD30, RAD30A, XPV EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens) Explore Q9Y253 Go to UniProtKB: Q9Y253
PHAROS: Q9Y253 GTEx: ENSG00000170734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y253
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPAPTPGPAPTPGPAPCPGPCPT)-3')	B [auth T]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APGPCPGPTPCPAPT*())-3')	C [auth P]	8	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HF4 (Subject of Investigation/LOI) Query on HF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-CCXZUQQUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.848	α = 90
b = 98.848	β = 90
c = 82.048	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Chang, C.

Gao, Y.

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR190046
Welch Foundation	United States	C-2033-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008280