Biology departement

Master 1 biochimistry

Structural biology

RCSB PDB
“STRUCTURE OF THE
HUMAN TELOMERASE
THUMB DOMAIN”

By: Kaid Seloua

Module manager: Mr.Rachedi

27-12-2018
 Introduction 
The Protein Data Bank (PDB) is a database for the three-dimensional
structural data of large biological molecules, such as proteins and
nucleic acids. The data, typically obtained by X-ray crystallography,
NMR spectroscopy, or, increasingly, cryo-electron microscopy, and
submitted by biologists and biochemists from around the world, are
freely accessible on the Internet via the websites of its member
organizations (PDBe,[1] PDBj,[2] and RCSB[3]). The PDB is overseen
by an organization called the Worldwide Protein Data Bank, wwPDB.

Contains:

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 DIFINITIONs
RCSB PDB:
Research Collaboratory for Structural Bioinformatics
The RCSB PDB supports a website where visitors can perform simple
and complex queries on the data, analyze, and visualize the results.
Details about the history, function, progress of macromolecules.

*RCSB is an American web site*

The telomere and telomerase:

Telomeres, the protective cap on the end of linear eukaryotic
chromosomes, are composed of short G-rich DNA repeats bound by
sequence-specific proteins ,The telomeres of unicellular eukaryotes
and of the germ cells of multicellular organisms are maintained by
the ribonucleoprotein enzyme telomerase, which was first identified
in the ciliated protozoan Tetrahymena thermophila . Telomerase
activity has been detected in ∼90% of human cancers, providing a
telomere maintenance mechanism that is necessary for their
unlimited growth.

The thumb domain:

The protein subunit, TERT, consists of several domains (TEN, TRBD,RT Fingers,
Palm and thumb) organized into a closed, ring configuration, generating a large
cavity in the interior of the ring and where the RNA template and the DNA bind
during telomere elongation. The closed configuration of the TERT ring is
stabilized by extensive interactions Between the thumb and TRBD domains as
well as by protein - RNA interactions

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The general information about human telomerase reverse
transcriptase

Go to the web site: http://pdb.rcsb.org

Write our protein of interest which is “telomerase reverse

transcriptase”

In the refinement choose Homo sapiens

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 Choose the “STRUCTURE OF THE HUMAN TELOMERASE THUMB
DOMAIN”

Classification: TRANSFERASE

Organism(s): Homo sapiens

Deposited: 2017-01-10 Released: 2017-02-08

Deposition Author(s): Skordalakes, E., Hoffman, H.

Funding Organization(s): National Institutes of Health/National

Cancer Institute

Method: X-RAY DIFFRACTION

Resolution: 2.31 Å

R-Value Free: 0.209

R-Value Work: 0.197

X-ray diffraction: X-ray diffraction (XRD) is one of the most important non-
destructive tools to analyze all kinds of matter—ranging from fluids, to
powders and crystals. From research to production and engineering, XRD is an
indispensable method for materials characterization and quality control. Rigaku
has developed a range of X-ray diffractometers, in co-operation with academic
and industrial users, which provide the most technically advanced versatile and
cost-effective diffraction solutions available today.

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The secondary structure of the human telomerase thumb domain

The secondary structure

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 Alpha helix:
7 to 27
37 to 60
72 to 95
112 to 127
129 to 149
155 to 163
 3/10 helix :
69 to 30
69 to 71 127 to 129
 Turns :
35 to 37
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67 to 68
95 to 97
99 to 101
149 to 151

*-there is no beta structure- *

The tertiary structure:

Ramachandran plot

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96.8% of all residues were in favored regions
3.2% of all residues were in forbidden regen