Primary Citation PubMed: 9428769
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Global analysis of posttranslational protein arginylation.
(2007) PLoS Biol 5
PubMed: 17896865 | PubMedCentral: PMC1988855 | DOI: 10.1371/journal.pbio.0050258
Figure 6 Structural Models of Proteins Regulated by Arginylation Three-dimensional structures of proteins downloaded from the National Center for Biotechnology Information structure database at http:/... www.ncbi.nlm.nih.gov/ (PDB identifiers 1HLU for beta actin, 1TUB for tubulin, 1DXT for hemoglobin, and 1ZNQ for GADPH) with arginylated positions highlighted in yellow within the polypeptide chains and marked with red letters R. Alpha and beta for tubulin indicate the corresponding polypeptide chains.
To further assess the possible role of arginylation in modulating the activity of the proteins found on our list, we selected a few targets from our list whose biological role is well characterized and for which three-dimensional structures are available in a public database, including non-muscle actin (PDB identifier 1HLU), tubulin (1TUB), hemoglobin (1DXT), GAPDH (1ZNQ), ARP3 (as part of ARP2/3 complex, 1K8K), 8-kDa dynein light chain (1PWK), and fragment of calmodulin in complex with spectrin (2FOT).
Publication Year: 2007
MAP2 and tau bind longitudinally along the outer ridges of microtubule protofilaments.
(2002) J Cell Biol 157
PubMed: 12082079 | PubMedCentral: PMC2173547 | DOI: 10.1083/jcb.200201048
(A) View from the minus end of the protofilament structure (Protein Data Bank identification no. 1TUB) docked into the microtubule map (blue wire frame).
Tubulin αβ dimer coordinates ( Nogales et al., 1998 ; Protein Data Bank identification no. 1TUB) were manually docked into the undecorated microtubule 3D map using the program O ( Jones et al., 1991 ) according to the previously published orientation ( Nogales et al., 1999 ).
Publication Year: 2002
Distinct conformations of the kinesin Unc104 neck regulate a monomer to dimer motor transition.
(2003) J Cell Biol 163
PubMed: 14638858 | PubMedCentral: PMC2173678 | DOI: 10.1083/jcb.200308020
Modeling The tubulin dimer structure ( Nogales et al., 1998 ; PDB id 1TUB) was manually docked into the undecorated microtubule 3D map using the program O ( Jones et al., 1991 ), using the hig... resolution microtubule model as a guide ( Li et al., 2002 ).
Publication Year: 2003
Orientation and structure of the Ndc80 complex on the microtubule lattice.
(2008) J Cell Biol 182
PubMed: 18794333 | PubMedCentral: PMC2542468 | DOI: 10.1083/jcb.200804170
(A and B) A model of a microtubule protofilament made from the tubulin dimer (PDB 1TUB) was docked into a single protofilament cut from the Ndc80/Nuf2 microtubule EM map.
To determine the relationship between the Ndc80/Nuf2 dimer and the microtubule, we docked a model of the high resolution polymerized form of the tubulin dimer (PDB 1TUB) into the electron density as described previously by Nogales et al. (1999) .
To verify the positioning of kinesin versus the Ncd80/Nuf2 dimer, we overlapped a model of the crystal structure of Ncd-600k (PDB 1N6M) bound to the tubulin dimer (PDB 1TUB) as described previously by Endres et al. (2006) with our Ncd80/Nuf2 map ( Fig. 4 A , red dashed line).
Publication Year: 2008
The roles of beta-tubulin mutations and isotype expression in acquired drug resistance.
(2007) Cancer Inform 3
PubMed: 19455242 | PubMedCentral: PMC2675838 | DOI: null
The first tubulin structure, 1TUB, was crystallized as a flat Zn 2+ induced sheet of antiparallel protofilament-like end-to-end α/β dimer repeats, using docetaxel as a stabilizing agen... ( Nogales et al. 1998 ).
A new model for binding of kinesin 13 to curved microtubule protofilaments.
(2009) J Cell Biol 185
PubMed: 19332892 | PubMedCentral: PMC2700504 | DOI: 10.1083/jcb.200812052
(C) Model of the crystal structures of truncated NM (Protein Data Bank reference codes 2HEH and 1v8k) fitted onto straight (Protein Data Bank reference code 1tub) and bent tubulin (Protein Data Bank r... ference code 1sa0).
Publication Year: 2009
Cytoskeletal signaling: is memory encoded in microtubule lattices by CaMKII phosphorylation?
(2012) PLoS Comput Biol 8
PubMed: 22412364 | PubMedCentral: PMC3297561 | DOI: 10.1371/journal.pcbi.1002421
Tubulin and Microtubule Lattice Modeling PDB tubulin protein structure 1JFF  was repaired by adding missing residues from 1TUB  .
Publication Year: 2012
The zinc dyshomeostasis hypothesis of Alzheimer's disease.
(2012) PLoS One 7
PubMed: 22457776 | PubMedCentral: PMC3311647 | DOI: 10.1371/journal.pone.0033552
Methods Molecular Modeling of Theoretical Zinc Binding Sites on Tubulin Tubulin and MT Modeling The Protein Data Bank (PDB)  crystal structure of bovine brain tubulin 1JFF  was repaired via ho... ology modeling by adding missing residues from 1TUB  using MODELLER 9V6  .
Difficulties in generating specific antibodies for immunohistochemical detection of nitrosylated tubulins.
(2013) PLoS One 8
PubMed: 23840827 | PubMedCentral: PMC3696116 | DOI: 10.1371/journal.pone.0068168
The 3D structure of the α/β-tubulin heterodimer was taken from the protein data bank (PDB ID: 1TUB)  .
Publication Year: 2013
A direct interaction between leucine-rich repeat kinase 2 and specific ?-tubulin isoforms regulates tubulin acetylation.
(2014) J Biol Chem 289
PubMed: 24275654 | PubMedCentral: PMC3887213 | DOI: 10.1074/jbc.M113.507913
Because this compound alters the surface conformation adjacent to the LRRK2 binding site, the remaining models used the structure of unbound α/β-tubulin dimers (PDB 1TUB ) ( 45 ).
Publication Year: 2014
The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.
(2014) PLoS Comput Biol 10
PubMed: 24516374 | PubMedCentral: PMC3916224 | DOI: 10.1371/journal.pcbi.1003464
Missing residues of the α-H1-S2 loop (residues α:35–60) were incorporated using those in Nogales et al.'s earlier Zn 2+ -induced protofilament model (PDB entry 1TUB  ).
Kinesin-14 and kinesin-5 antagonistically regulate microtubule nucleation by ?-TuRC in yeast and human cells.
(2014) Nat Commun 5
PubMed: 25348260 | PubMedCentral: PMC4220466 | DOI: 10.1038/ncomms6339
Structural analysis PyMol molecular visualization software (V1.5) was used for structural analysis of the conserved α-β-tubulin heterodimer 1TUB 10 and conserved γ-tubulin mono... er 1Z5V 6 11 14 69 in Fig. 3 .
PubMed ID is not available.
Published in 2015
The central tubulin dimer of the 3×3 lattice in each case was separated and was repaired by the addition of missing residues (Residue 1 in β -tubulin and residues 1,39 to 48, 440 in ... 003b1; -tubulin) from the PDB structure 1TUB [ 36 ], using MOE.
Publication Year: 2015
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