spacer
spacer

PDBsum entry 1z5w

Go to PDB code: 
protein ligands metals links
Structural protein PDB id
1z5w
Jmol
Contents
Protein chain
409 a.a. *
Ligands
GTP
Metals
_MG
* Residue conservation analysis
PDB id:
1z5w
Name: Structural protein
Title: Crystal structure of gamma-tubulin bound to gtp
Structure: Tubulin gamma-1 chain. Chain: a. Synonym: gamma-1 tubulin, gamma-tubulin complex component 1, gcp-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: tubg1, tubg. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Resolution:
3.00Å     R-factor:   0.247     R-free:   0.309
Authors: H.A.Aldaz,L.M.Rice,T.Stearns,D.A.Agard
Key ref:
H.Aldaz et al. (2005). Insights into microtubule nucleation from the crystal structure of human gamma-tubulin. Nature, 435, 523-527. PubMed id: 15917813 DOI: 10.1038/nature03586
Date:
20-Mar-05     Release date:   31-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23258  (TBG1_HUMAN) -  Tubulin gamma-1 chain
Seq:
Struc:
451 a.a.
409 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cilium basal body   20 terms 
  Biological process     organelle organization   10 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1038/nature03586 Nature 435:523-527 (2005)
PubMed id: 15917813  
 
 
Insights into microtubule nucleation from the crystal structure of human gamma-tubulin.
H.Aldaz, L.M.Rice, T.Stearns, D.A.Agard.
 
  ABSTRACT  
 
Microtubules are hollow polymers of alphabeta-tubulin that show GTP-dependent assembly dynamics and comprise a critical part of the eukaryotic cytoskeleton. Initiation of new microtubules in vivo requires gamma-tubulin, organized as an oligomer within the 2.2-MDa gamma-tubulin ring complex (gamma-TuRC) of higher eukaryotes. Structural insight is lacking regarding gamma-tubulin, its oligomerization and how it promotes microtubule assembly. Here we report the 2.7-A crystal structure of human gamma-tubulin bound to GTP-gammaS (a non-hydrolysable GTP analogue). We observe a 'curved' conformation for gamma-tubulin-GTPgammaS, similar to that seen for GDP-bound, unpolymerized alphabeta-tubulin. Tubulins are thought to represent a distinct class of GTP-binding proteins, and conformational switching in gamma-tubulin might differ from the nucleotide-dependent switching of signalling GTPases. A crystal packing interaction replicates the lateral contacts between alpha- and beta-tubulins in the microtubule, and this association probably forms the basis for gamma-tubulin oligomerization within the gamma-TuRC. Laterally associated gamma-tubulins in the gamma-TuRC might promote microtubule nucleation by providing a template that enhances the intrinsically weak lateral interaction between alphabeta-tubulin heterodimers. Because they are dimeric, alphabeta-tubulins cannot form microtubule-like lateral associations in the curved conformation. The lateral array of gamma-tubulins we observe in the crystal reveals a unique functional property of a monomeric tubulin.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: bold gamma--tubulin adopts a curved conformation. Structural superposition of -tubulin conformations onto -tubulin using the rigid N-terminal domain. a, The -tubulin structure (blue) and the curved -tubulin structure (green) share a similar arrangement of the H6 -H7 segment (left) and of intermediate domains (right). b, The -tubulin structure (blue) and the straight -tubulin structure (pink) show characteristic differences in the orientation of the H6 -H7 segment (left) and the intermediate domain (right). c, Comparison between the curved (green) and straight (pink) -tubulin conformations, illustrating the characteristic differences in the H6 -H7 segment (left) and the intermediate domain (right).
Figure 3.
Figure 3: Lateral interactions between bold gamma--tubulins resemble lateral interactions in the microtubule lattice. a, 'Minus end' views of laterally interacting -tubulins in the microtubule lattice (green) (K. Downing, personal communication), and laterally interacting -tubulins in the crystal (blue). Contact regions between monomers are indicated by the grey surfaces on the central monomer. b, Comparative 'outside' views of the same interactions, showing a similar pitch for both. c, Lateral interaction regions of -tubulin in the microtubule lattice (green) and -tubulin in the crystal (blue) are indicated on the molecular surface. Microtubule and -tubulin crystal interaction footprints are very similar. d, Comparison of the buried surface area (in 2) at each position for -tubulin lateral interactions in the microtubule lattice (left) and -tubulin crystal interactions (right). Virtually identical regions of the structure are involved in both interactions.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 435, 523-527) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23086237 S.Lawo, M.Hasegan, G.D.Gupta, and L.Pelletier (2012).
Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material.
  Nat Cell Biol, 14, 1148-1158.  
21397191 A.Grafmüller, and G.A.Voth (2011).
Intrinsic bending of microtubule protofilaments.
  Structure, 19, 409-417.  
21993292 J.M.Kollman, A.Merdes, L.Mourey, and D.A.Agard (2011).
Microtubule nucleation by γ-tubulin complexes.
  Nat Rev Mol Cell Biol, 12, 709-721.  
21208439 S.A.Endow, and M.A.Hallen (2011).
Anastral spindle assembly and γ-tubulin in Drosophila oocytes.
  BMC Cell Biol, 12, 1.  
21473851 T.Hubert, S.Perdu, J.Vandekerckhove, and J.Gettemans (2011).
γ-Tubulin localizes at actin-based membrane protrusions and inhibits formation of stress-fibers.
  Biochem Biophys Res Commun, 408, 248-252.  
21725292 V.Guillet, M.Knibiehler, L.Gregory-Pauron, M.H.Remy, C.Chemin, B.Raynaud-Messina, C.Bon, J.M.Kollman, D.A.Agard, A.Merdes, and L.Mourey (2011).
Crystal structure of γ-tubulin complex protein GCP4 provides insight into microtubule nucleation.
  Nat Struct Mol Biol, 18, 915-919.
PDB code: 3rip
20631709 J.M.Kollman, J.K.Polka, A.Zelter, T.N.Davis, and D.A.Agard (2010).
Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry.
  Nature, 466, 879-882.  
20386893 K.M.Tyler, G.K.Wagner, Q.Wu, and K.T.Huber (2010).
Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins.
  J Mol Evol, 70, 395-402.  
20736306 S.Bahmanyar, E.L.Guiney, E.M.Hatch, W.J.Nelson, and A.I.Barth (2010).
Formation of extra centrosomal structures is dependent on beta-catenin.
  J Cell Sci, 123, 3125-3135.  
19648910 M.Alvarado-Kristensson, M.J.Rodríguez, V.Silió, J.M.Valpuesta, and A.C.Carrera (2009).
SADB phosphorylation of gamma-tubulin regulates centrosome duplication.
  Nat Cell Biol, 11, 1081-1092.  
19565362 R.H.Wade (2009).
On and around microtubules: an overview.
  Mol Biotechnol, 43, 177-191.  
18621829 A.S.Zeiger, and B.E.Layton (2008).
Molecular modeling of the axial and circumferential elastic moduli of tubulin.
  Biophys J, 95, 3606-3618.  
18003974 C.Wiese (2008).
Distinct Dgrip84 Isoforms Correlate with Distinct {gamma}-Tubulins in Drosophila.
  Mol Biol Cell, 19, 368-377.  
18502809 E.R.Miraldi, P.J.Thomas, and L.Romberg (2008).
Allosteric models for cooperative polymerization of linear polymers.
  Biophys J, 95, 2470-2486.  
18959762 F.Marziale, S.Pucciarelli, P.Ballarini, R.Melki, A.Uzun, V.A.Ilyin, H.W.Detrich, and C.Miceli (2008).
Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature.
  FEBS J, 275, 5367-5382.  
17978090 J.M.Kollman, A.Zelter, E.G.Muller, B.Fox, L.M.Rice, T.N.Davis, and D.A.Agard (2008).
The Structure of the {gamma}-Tubulin Small Complex: Implications of Its Architecture and Flexibility for Microtubule Nucleation.
  Mol Biol Cell, 19, 207-215.  
18388201 L.M.Rice, E.A.Montabana, and D.A.Agard (2008).
The lattice as allosteric effector: structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly.
  Proc Natl Acad Sci U S A, 105, 5378-5383.
PDB code: 3cb2
18567627 M.A.Hallen, J.Ho, C.D.Yankel, and S.A.Endow (2008).
Fluorescence recovery kinetic analysis of gamma-tubulin binding to the mitotic spindle.
  Biophys J, 95, 3048-3058.  
18780727 M.Vázquez, M.T.Cooper, M.Zurita, and J.A.Kennison (2008).
gammaTub23C interacts genetically with brahma chromatin-remodeling complexes in Drosophila melanogaster.
  Genetics, 180, 835-843.  
17178454 B.Raynaud-Messina, and A.Merdes (2007).
Gamma-tubulin complexes and microtubule organization.
  Curr Opin Cell Biol, 19, 24-30.  
17406983 C.D.Katsetos, E.Dráberová, B.Smejkalová, G.Reddy, L.Bertrand, J.P.de Chadarévian, A.Legido, J.Nissanov, P.W.Baas, and P.Dráber (2007).
Class III beta-tubulin and gamma-tubulin are co-expressed and form complexes in human glioblastoma cells.
  Neurochem Res, 32, 1387-1398.  
17977836 S.Huecas, C.Schaffner-Barbero, W.García, H.Yébenes, J.M.Palacios, J.F.Díaz, M.Menéndez, and J.M.Andreu (2007).
The interactions of cell division protein FtsZ with guanine nucleotides.
  J Biol Chem, 282, 37515-37528.  
16957770 C.A.Moores, M.Perderiset, C.Kappeler, S.Kain, D.Drummond, S.J.Perkins, J.Chelly, R.Cross, A.Houdusse, and F.Francis (2006).
Distinct roles of doublecortin modulating the microtubule cytoskeleton.
  EMBO J, 25, 4448-4457.  
16941085 E.J.Carpenter, J.T.Huzil, R.F.Ludueña, and J.A.Tuszynski (2006).
Homology modeling of tubulin: influence predictions for microtubule's biophysical properties.
  Eur Biophys J, 36, 35-43.  
16549346 E.Nogales, and H.W.Wang (2006).
Structural mechanisms underlying nucleotide-dependent self-assembly of tubulin and its relatives.
  Curr Opin Struct Biol, 16, 221-229.  
16603504 J.van Gestel, and S.W.de Leeuw (2006).
A statistical-mechanical theory of fibril formation in dilute protein solutions.
  Biophys J, 90, 3134-3145.  
17084690 K.Ribbeck, and T.J.Mitchison (2006).
Meiotic spindle: sculpted by severing.
  Curr Biol, 16, R923-R925.  
16899509 L.Cuschieri, R.Miller, and J.Vogel (2006).
Gamma-tubulin is required for proper recruitment and assembly of Kar9-Bim1 complexes in budding yeast.
  Mol Biol Cell, 17, 4420-4434.  
16166645 S.Sankaran, L.M.Starita, A.C.Groen, M.J.Ko, and J.D.Parvin (2005).
Centrosomal microtubule nucleation activity is inhibited by BRCA1-dependent ubiquitination.
  Mol Cell Biol, 25, 8656-8668.  
16344310 Y.Shang, C.C.Tsao, and M.A.Gorovsky (2005).
Mutational analyses reveal a novel function of the nucleotide-binding domain of gamma-tubulin in the regulation of basal body biogenesis.
  J Cell Biol, 171, 1035-1044.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.