loon.data: Data Used to Illustrate 'Loon' Functionality

Description Format Author(s) Source References See Also

Contains three dimensional structure of the GAL4 protein of Saccharomyces Cerevisiae (or Baker's Yeast) recognizing and binding to a Deoxyribonucleic acid (DNA) sequence.

There are effectively two molecules here (a protein and DNA) binding together. It is a transcription/DNA complex within Saccharomyces Cerevisiae.

From Marmorstein et al (1992):

"The yeast protein GAL4 activates transcription of genes required for catabolism of galactose and melibiose. The DNA sequences recognized by GAL4 are 17 base pairs (bp) in length and each site binds a dimer of the protein."

and

"The protein fragment binds to its DNA site as a symmetrical dimer. Each subunit folds into three distinct modules: a compact, metal-binding domain (residues 8-40), an extended linker (41-49), and an a-helical dimerization element ( 50-64). Residues 1-7 and 65-66 are disordered. An overall view of the complex shows that a large part of the DNA major groove is not contacted by the protein. The DNA is relatively straight. A metal domain lies in the major groove near each end of the DNA fragment. The paired parallel helices of the dimerization element project away from the DNA along the 2-fold axis of the complex. The metal-binding domain contacts three DNA base pairs in the major groove, and we therefore refer to it as a ‘recognition module.’ ...

The recognition module is held together by two metal ions, tetrahedrally coordinated by the six cysteines. Two of the cysteines (11 and 28) ligate both metals, creating a ‘binuclear cluster’ ... "

See Marmorstein et al (1992) for more on the geometry.

The source of most data here is Protein Data Bank (PDB) entry 1d66.

All coordinates, chains, residues, backbone atom identities, and displacements are taken from the PDB entry. Not included here are those entries from the PDB record which simply identify the terminus of each of the chains D, E, A, and B. Each of these 'TER' entries contain no coordinates since it simply marks the end of its chain.

Values were determined by X-ray crystallography at 2.7 Angstrom resolution.

These values have been supplemented with variable values from a variety of sources so as to help in the identification of components of the molecular structure.

A data frame with 1762 rows and 14 variates:

group: One of 'ATOM' or 'HETATM'. Here 'ATOM' indicates an atom having a standard residue of the protein; 'HETATM' (hetero atom) indicates one either having a non-standard residue of protein, or one in a group of a different kind such as carbohydrates, substrates, ligands, solvent, or metal ions. In the 'SCmolecule', these will be either a water molecule 'HOH' or a Cadmium ion 'CD'.
id: Identification number of the backbone atom as given in the protein data bank (PDB).
label: Atom identifier. These follow a standard used by the PDB. The first character is the element abbreviation of the backbone atom. The remaining characters of the nomenclature identify which of the atoms of that type are being referred to in the structure.
residue: A two or three letter abbreviation naming the residue attached to that atom.
chain: Identifies a chain of atoms. These are polypeptide or DNA chains.
sequence: Order in which that bakbone atom appears in its chain.
x, y, z: Coordinates of the bakbone atom in three-dimensonal space.
displacement: Equivalent isotropic displacement factor; also sometimes earlier called a temperature factor. It is a measure of the possible coordinate location displacement of an atom from any source. Displacements could arise, for example, from atomic vibrations, such as (large) molecular motion or (smaller) internal vibrations, or any of a variety of sources of disorder. This is recorded as a spherical Gaussian (isotropic) measure of the variability of the location by the average eigen-value of a variance-covariance matrix.
type: The element symbol of the backbone atom.
mass: Atomic mass of the backbone atom.
residueType: Type of the residue.
residueName: Full name of the residue.

R.W. Oldford

https://www.rcsb.org/3d-view/1D66/. https://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66

Ronen Marmorstein, Michael Carey, Mark Ptashne, and Stephen C. Harrison (1992) "DNA recognition by GAL4: structure of a protein-DNA complex", Nature, 356, pp. 408-414.

John L. Markley, Ad Bax, Yoji Arata, C. W. Hilbers, Robert Kaptein, Brian D. Syke, Peter E. Wright, and Kurt Wuthrich (1998) "Recommendations for the presentation of NMR structures of proteins and nucleic acids", European Journal of Biochemistry, 256, pp. 1-15.

Reinhard X. Fischer and Ekkehart Tilmanns (1988) "The equivalent isotropic displacement factor", Acta Crystallographica C44, pp. 775-776.

K.N. Truebloof, H.-B. Burgi, H. Burzlaff, J.D. Dunitz, C.M. Gramaccioli, H.H. Schulz, U. Shmueli, and S.C. Abrahams (1996) "Atomic displacement parameter nomenclature" Acta Crystallographica A52, pp. 770-781.

elements igg1

rwoldford/loon.data documentation built on May 17, 2021, 7:45 a.m.