8E66 | pdb_00008e66

ETV6 H396Y variant bound to DNA containing the sequence GGAA

PDB DOI: https://doi.org/10.2210/pdb8E66/pdb
NAKB: 8E66

Classification: DNA BINDING PROTEIN/DNA
Organism(s): synthetic construct, Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-08-22 Released: 2023-08-30
Deposition Author(s): Scheu, K., Chan, A.C., Murphy, M.E., McIntosh, L.P.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.255 (Depositor), 0.250 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The functional role of histidine within the ETV6 ETS domain

Scheu, K., Chan, A.C., Murphy, M.E., McIntosh, L.P.

To be published.

Macromolecule Content

Total Structure Weight: 42.86 kDa
Atom Count: 2,936
Modeled Residue Count: 244
Deposited Residue Count: 260
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6	C [auth A], F	100	Mus musculus	Mutation(s): 1 Gene Names: Etv6
UniProt & NIH Common Fund Data Resources
Find proteins for P97360 (Mus musculus) Explore P97360 Go to UniProtKB: P97360
IMPC: MGI:109336
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P97360
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
GGAA-containing 15 bp DNA	A [auth B], D	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
Complementary 15 bp strand	B [auth C], E	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255 (Depositor), 0.250 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.841	α = 90
b = 94.685	β = 94.76
c = 76.259	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.