5YJ3

Crystal structure of TZAP and telomeric DNA complex

PDB DOI: https://doi.org/10.2210/pdb5YJ3/pdb
NAKB: 5YJ3

Classification: DNA BINDING PROTEIN/DNA
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-07 Released: 2017-12-06
Deposition Author(s): Li, F., Zhao, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.268
R-Value Work: 0.226
R-Value Observed: 0.228

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The 11th C2H2 zinc finger and an adjacent C-terminal arm are responsible for TZAP recognition of telomeric DNA.

Zhao, Y., Zhang, G., He, C., Mei, Y., Shi, Y., Li, F.

(2018) Cell Res 28: 130-134

PubMed: 29134956 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2017.141
Primary Citation of Related Structures:
5YJ3

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

Macromolecule Content

Total Structure Weight: 37.35 kDa
Atom Count: 1,829
Modelled Residue Count: 172
Deposited Residue Count: 250
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
Telomere zinc finger-associated protein	C, D	107	Homo sapiens	Mutation(s): 0 Gene Names: ZBTB48, HKR3, TZAP, ZNF855
UniProt & NIH Common Fund Data Resources
Find proteins for P10074 (Homo sapiens) Explore P10074 Go to UniProtKB: P10074
PHAROS: P10074 GTEx: ENSG00000204859
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10074
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPCPTPAPAPCPCPCPTPAPAPCPCPCPTPAPAPC)-3')	A	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPGPTPTPAPGPGPGPTPTPAPGPGPGPTPTPAPG)-3')	B	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth D] SDF format, chain H [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D]	E [auth C], F [auth C], G [auth D], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.268
R-Value Work: 0.226
R-Value Observed: 0.228
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.713	α = 90
b = 56.713	β = 90
c = 226.229	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-12-06

Deposition Author(s):

Li, F.

Zhao, Y.

Revision History (Full details and data files)

Version 1.0: 2017-12-06
Type: Initial release
Version 1.1: 2018-01-17
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description