PDBsum entry: 1tub

Microtubules

PDB id: 1tub

Contents

Protein chains

440 a.a. *

427 a.a. *

Ligands

GTP

GDP

TXL

* Residue conservation analysis

PDB id:

1tub

Name:

Microtubules

Title:

Tubulin alpha-beta dimer, electron diffraction

Structure:

Tubulin. Chain: a. Tubulin. Chain: b

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: brain. Organ: brain

Biol. unit:

Dimer (from PDB file)

Authors:

E.Nogales,K.H.Downing

Key ref:

E.Nogales et al. (1998). Structure of the alpha beta tubulin dimer by electron crystallography. Nature, 391, 199-203. PubMed id: 9428769 DOI: 10.1038/34465

Date:

23-Sep-97 Release date: 07-Oct-98

Protein chain

P02550  (TBA1A_PIG) -  Tubulin alpha-1A chain

Seq: 451 a.a.

Struc: 440 a.a.*

Protein chain

P02554  (TBB_PIG) -  Tubulin beta chain

Seq: 445 a.a.

Struc: 427 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: protein complex (2 terms)
• Biological process: microtubule-based process (4 terms)
• Biochemical function: structural molecule activity (4 terms)

DOI no: 10.1038/34465

Nature 391:199-203 (1998)

PubMed id: 9428769

Structure of the alpha beta tubulin dimer by electron crystallography.

E.Nogales, S.G.Wolf, K.H.Downing.

ABSTRACT

The alphabeta tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is nonexchangeable when it is bound in the alpha subunit, or N site, and exchangeable when bound in the beta subunit, or E site. The alpha- and beta-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of posttranslational modifications. Limited sequence homology has been found with the proteins FtsZ and Misato, which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the alphabeta tubulin dimer fitted to a 3.7-A density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.

Selected figure(s)

Figure 3.
Figure 3 Sequences of pig brain - and -tubulin28 used in the model (in the absence of tubulin sequences from cow we have used its closest known relative). Secondary structure elements are indicated and labelled as for Fig. 4. The tubulin preparations used in our experiments contained a mixture of isotypes. Most of the differences between isotypes are located at the extreme C terminus, which is not visible in our density. In most of the other positions of isotype differences, we arbitrarily chose the residue most similar to the other monomer.

Figure 4.
Figure 4 Ribbon diagram of the tubulin dimer showing -tubulin with bound GTP (top), and -tubulin containing GDP and taxotere (bottom). Labels for strands (in the -subunit) and helices (in the -subunit) are included. The arrow indicates the direction of the protofilament and microtubule axis. a, Stereo front view from the putative outside of the microtubule; b, back view from the putative inside of the microtubule; c, side view. Figures produced with AVS (Advanced Visual; ribbon module from M. Carson and A. Shah). The in-out orientation was determined by reference to reconstructions of intact microtubules9. Such reconstructions show prominent longitudinal ridge on the outside, which in our model would be formed by H11, H12 and the loop between H10 and B9, and shallow inside grooves giving the protofilament a bumpy appearance, corresponding in our model to H1, B3 and the long loops in the N-terminal domain. This represents the most likely arrangement of the dimer, because it buries the nucleotide that is at the non-exchangeable site in (see text). For the nucleotide in to be exchangeable at the plus end of a microtubule, the bottom of the figure would correspond to the plus end. We previously presumed the opposite orientation, based on a comparison of the zinc sheets in negatively stained, stain-glucose, and tannin-glucose embedding, with projection maps of open microtubules of known polarity in negative stain9. Some ambiguity in that determination may be introduced by uncertainty about the exact rotational alignment of the protofilament in the sheets with respect to those in open microtubules and by stain artefacts. The polarity with the plus end down would be consistent with experiments that located the -subunit at the plus end of the microtubule^29 and the -subunit at the minus end^30. Circles in b indicate the positions of Cys 241 and Cys 356, separated by about 8 Å.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 391, 199-203) copyright 1998.

Figures were selected by an automated process.