Citations in PubMed

Primary Citation PubMed: 11700061 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 46

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Mutations in alpha-tubulin cause abnormal neuronal migration in mice and lissencephaly in humans.

(2007) Cell 128

PubMed: 17218254 | PubMedCentral: PMC1885944 | DOI: 10.1016/j.cell.2006.12.017

Figure 7 Mapping of the Mutations onto the α-Tubulin Structure (A) The structure of α-tubulin (pdb: 1JFF).

Publication Year: 2007

The beginning of kinesin's force-generating cycle visualized at 9-A resolution.

(2007) J Cell Biol 177

PubMed: 17470637 | PubMedCentral: PMC2064809 | DOI: 10.1083/jcb.200612090

The C terminus of kinesin's helix α3 is also out of density, possibly correlated to a rearrangement of switch I. To evaluate tubulin's secondary structure elements, the coordinates of bovine t... bulin (Protein Data Bank [PDB] ID 1JFF; Lowe et al., 2001 ) were fitted into the cryo-EM map using cross-correlation implemented in Fourier space (see Materials and methods).

Publication Year: 2007

Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice.

(2003) J Cell Biol 163

PubMed: 14662742 | PubMedCentral: PMC2173608 | DOI: 10.1083/jcb.200304034

αβ-tubulin dimer atomic coordinates ( Löwe et al., 2001 ; Protein Data Bank identification number 1JFF) and the human conventional kinesin motor core atomic coordinates... ( Kull et al., 1996 ; Protein Data Bank identification number 1BG2) were manually docked into the pKinI-ADP microtubule map using AVS (Advanced Visual Systems, Inc.).

Publication Year: 2003

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information.

(2008) PLoS Comput Biol 4

PubMed: 18818722 | PubMedCentral: PMC2526173 | DOI: 10.1371/journal.pcbi.1000181

The predicted structure is generated by homology-modeling techniques using the eukaryotic α/β tubulin dimer (PDB identifier: 1jff) as the template.

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

A solvent accessible surface was drawn onto the α/β-tubulin heterodimer obtained by Nogales et al. 2001 (PDB identifier 1JFF).

Structures of the paclitaxel (PTX), colchicine (CN) and vinblastine (VLB) from structural files 1JFF, 1SA0 and 1Z2B have been superimposed and fit back onto the 1SA0 structure to obtain the relative positioning of each drug within the protofilament.

This was done as the structural file, 1JFF, does not contain any of these residues.

The columns representing drug interactions indicate residues in which any atom is within 6 Å of any atom within the bound drug molecule from structural files 1JFF, 1SA0 and 1Z2B for Paclitaxel (PTX), Colchicine (CN) and Vinblastine (VLB) respectively.

Publication Year: 2007

Motor neuron synapse and axon defects in a C. elegans alpha-tubulin mutant.

(2010) PLoS One 5

PubMed: 20300184 | PubMedCentral: PMC2836382 | DOI: 10.1371/journal.pone.0009655

(D) Crystal structure of alpha-beta tubulin dimer generated by Polyview based on Nogales et al, 1998 and Lowe et al., 2001 (PDB#1JFF).

Publication Year: 2010

TUBA1A mutations cause wide spectrum lissencephaly (smooth brain) and suggest that multiple neuronal migration pathways converge on alpha tubulins.

(2010) Hum Mol Genet 19

PubMed: 20466733 | PubMedCentral: PMC2893812 | DOI: 10.1093/hmg/ddq182

The former model was based on docking of the α- and β-tubulin heterodimer crystal structure (PDB id: 1JFF) ( 31 ) into the cryo electron microscopy (cryoEM) map of the intact microtubu... es at 8 Å resolution ( 32 ) (coordinates kindly provided by Ken Downing, Life Sciences Division, Berkeley Lab), while the latter was based on docking of the same structure (PDB id: 1JFF) in addition to the kinesin KIF1A motor domain crystal structure (PDB id: 1VFV) into the cryoEM map of the complex in an AMPPNP (5′-adenylyl-β,γ-imidodiphosphate) form at 10 Å resolution (PDB id: 2HXF) ( 33 ).

Publication Year: 2010

Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution.

(2010) J Cell Biol 191

PubMed: 20974813 | PubMedCentral: PMC3003314 | DOI: 10.1083/jcb.201007081

The quality of the fit was assessed by cross-correlation between our structure and simulated 8 Å maps for each PDB: 1JFF β-tubulin gave the best score of 0.651 in our β-tubulin... density (3HKE β-tubulin chain B gave 0.599); α-tubulin from 1JFF and 3HKE chain A scored similarly, 0.605 and 0.607, against 0.614 for a chimeric structure (3HKE chain A residues 31–61, 69–92, and 275–298 substituted to corresponding ones in 1JFF chain A).

(D) Sections of a sequence alignment of the main isoforms of bovine tubulin used in our structure (1JFF-A and 1JFF-B), and of other human tubulin isoforms ( TUBA1A , GenBank/EMBL/DDBJ accession no. 7846; TUBA3D , accession no. 113457; TUBB2B , accession no. 347733; TUBB3 , accession no. 10381).

α-tubulins are highlighted in blue and β-tubulins in cyan; sequence identities are highlighted in black; secondary structures of 1JFF-A are depicted below.

The atomic coordinates of the tubulin dimer calculated from zinc-induced 2D sheets (1JFF) fit very well into our structure ( Fig. 2 A ; Löwe et al., 2001 ).

The structures of α- and β-tubulin from zinc-induced sheets are fitted in the map (1JFF.

Crystal structures of α- and β-tubulin (1JFF.

Publication Year: 2010

Molecular characterization of beta-tubulin from Phakopsora pachyrhizi, the causal agent of Asian soybean rust.

(2010) Genet Mol Biol 33

PubMed: 21637494 | PubMedCentral: PMC3036848 | DOI: 10.1590/S1415-47572010005000040

GenBank accession numbers are: P. pachyrhizi (GU354165, this work), M. lini (Q9HFQ3), U. viciae-fabae (Q96TU8), P. sajor-caju (AAD21093), N. crassa (XP_957669), A. nidulans (XP_658786), S. cerevisiae ... V01296) and B. taurus (1JFF).

GenBank accession numbers are: P. pachyrhizi (GU354165, this work), M. lini (Q9HFQ3), U. viciae-fabae (Q96TU8), P. sajor-caju (AAD21093), N. crassa (XP_957669), A. nidulans (XP_658786), S. cerevisiae (V01296) and B. taurus (1JFF).

Publication Year: 2010

The Dam1 ring binds to the E-hook of tubulin and diffuses along the microtubule.

(2011) Mol Biol Cell 22

PubMed: 21169562 | PubMedCentral: PMC3038644 | DOI: 10.1091/mbc.E10-10-0841

By docking in the tubulin atomic structure (PDB: 1JFF), the polarity of the microtubule in the reconstruction, and therefore the polarity in each image, was determined.

Publication Year: 2011

Intraflagellar transport delivers tubulin isotypes to sensory cilium middle and distal segments.

(2011) Nat Cell Biol 13

PubMed: 21642982 | PubMedCentral: PMC3129367 | DOI: 10.1038/ncb2268

( c–d ) Inner (c) and outer (d) views of structure of predicted TBA-5 and TBB-4 heterodimer based on porcine brain tubulin dimer structure, 1JFF.

The heterodimeric structure of TBA-5 and TBB-4 was predicted with Modller9v6 using the porcine brain tubulin heterodimer structure 1JFF 33 as a template.

Publication Year: 2011

The evolution of the cytoskeleton.

(2011) J Cell Biol 194

PubMed: 21859859 | PubMedCentral: PMC3160578 | DOI: 10.1083/jcb.201102065

Structures of filament subunits are derived from the following Protein Data Bank accession numbers: 1W5A (FtsZ; Oliva et al., 2004 ), 1JFF (α/β-tubulin; Löwe et al., 2001 ), 1J... G (MreB; van den Ent et al., 2001 ), and 1YAG (actin; Vorobiev et al., 2003 ).

Publication Year: 2011

A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer.

(2011) Cancer Chemother Pharmacol 68

PubMed: 21340606 | PubMedCentral: PMC3180612 | DOI: 10.1007/s00280-011-1575-2

Docking of ITB-301 to microtubules Since microtubules are assembled from α- and β-tubulin dimers, in our studies, the structure of a model dimer was taken from the crystallographic dat... of α- and β-tubulin stabilized by paclitaxel [ 13 ], PDB code—1JFF.

Publication Year: 2011

Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(?-glutamyl-glutamate) paclitaxel conjugates.

(2011) J Mol Model 17

PubMed: 21360176 | PubMedCentral: PMC3203221 | DOI: 10.1007/s00894-011-0989-4

The initial structure for paclitaxel (PDB ID: 1JFF) was provided by the Protein Data Bank [ 25 ].

Publication Year: 2011

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography.

(2012) EMBO J 31

PubMed: 22157822 | PubMedCentral: PMC3273388 | DOI: 10.1038/emboj.2011.460

The pseudo-atomic model of the MT triplet was built based on an atomic structure of tubulin (PDB ID: 1JFF) by manually fitting into the EM density in program O ( Jones et al, 1991 ).

Publication Year: 2012

In silico study of fucoxanthin as a tumor cytotoxic agent.

(2012) J Pharm Bioallied Sci 4

PubMed: 22368399 | PubMedCentral: PMC3283957 | DOI: 10.4103/0975-7406.92733

The pdb files were 1JFF[ 20 ] (with paclitaxel ligand), 1SA0[ 21 ] (with colchicine ligand) and 1Z2B[ 22 ] (with vinblastine ligand).

Docking of fucoxanthin to subjected receptors were -6.2 (1RV1), -9.3 (1AQ1), -8.1 (1JFF), -9.2 (1SA0), and -7.2 (1Z2B) kcal/mol.

Publication Year: 2012

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 [79] was repaired by adding missing residues from 1TUB [80] .

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) [62] crystal structure of bovine brain tubulin 1JFF [38] was repaired via ho... ology modeling by adding missing residues from 1TUB [37] using MODELLER 9V6 [63] .

Tubulin-Zinc Binding Site Prediction To characterize zinc-binding sites on tubulin the minimized repaired 1JFF structure was run through the robust zinc protein-binding site prediction algorithm FEATURE: Metals [68] FEATURE: Metals structurally predicts zinc-binding sites based on coordination geometry trained on positive (known zinc binding sites) and negative (non-metal binding regions with characteristics of zinc binding sites) samples in conjunction with additional biophysical and biochemical properties averaged around the site of interest, with a 73.6% in unbound known proteins structures and 65.5% in protein structures determined from homology models.

Publication Year: 2012

Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin.

(2011) Nat Struct Mol Biol 18

PubMed: 22020298 | PubMedCentral: PMC3342691 | DOI: 10.1038/nsmb.2148

The crystallographic αβ-tubulin model (PDB ID 1JFF 44 ) was fit as a rigid-body into the SAXS envelope manually, and then locally adjusted using the fit-in-map algorithms implemented i... CHIMERA 60 .

(a) Pair-distance probability distributions, [ P(r) ], computed from the experimental SAXS data for the TTL–tubulin complex and the crystal structure of the tubulin dimer (1JFF.

Publication Year: 2011

Extent of structural asymmetry in homodimeric proteins: prevalence and relevance.

(2012) PLoS One 7

PubMed: 22629324 | PubMedCentral: PMC3358323 | DOI: 10.1371/journal.pone.0036688

Tubulin α and β subunits (GloA_Sc – 23.09; PDB – 1jff).

Publication Year: 2012

EBs recognize a nucleotide-dependent structural cap at growing microtubule ends.

(2012) Cell 149

PubMed: 22500803 | PubMedCentral: PMC3368265 | DOI: 10.1016/j.cell.2012.02.049

Pseudoatomic Model Building UCSF Chimera ( Pettersen et al., 2004 ) was used for visualization of 3D models and rigid-body fitting of atomic structures in the cryo-EM volume, using 1JFF.

Publication Year: 2012

Kar3Vik1, a member of the kinesin-14 superfamily, shows a novel kinesin microtubule binding pattern.

(2012) J Cell Biol 197

PubMed: 22734002 | PubMedCentral: PMC3384419 | DOI: 10.1083/jcb.201201132

1JFF ; Löwe et al., 2001 ) was docked manually into the electron density maps using UCSF Chimera ( Pettersen et al., 2004 ).

Publication Year: 2012

Conformational changes in tubulin in GMPCPP and GDP-taxol microtubules observed by cryoelectron microscopy.

(2012) J Cell Biol 198

PubMed: 22851320 | PubMedCentral: PMC3413364 | DOI: 10.1083/jcb.201201161

1JFF ) was fitted to our cryo-EM map (see Materials and methods for detail).

1JFF ; Löwe et al., 2001 ) as the initial model.

Publication Year: 2012

Understanding the basis of drug resistance of the mutants of ??-tubulin dimer via molecular dynamics simulations.

(2012) PLoS One 7

PubMed: 22879949 | PubMedCentral: PMC3413672 | DOI: 10.1371/journal.pone.0042351

Materials and Methods Molecular Dynamic Simulations of Wild-type and Mutants The atomic coordinates for wild-type (WT) tubulin dimer was obtained by engineering the crystal structure of taxol-bound tu... ulin, downloaded from protein data bank (PDB ID: 1JFF [13] ).

(a) Crystal structure of taxol bound αβ-tubulin dimer (1JFF).

Noting that the crystal structure used to initiate the MD simulations was determined at low resolution (e.g. in 1JFF, 15% of the rotamer and 10% of the backbone torsion angles were flagged as outliers), an extensive set of minimization and thermalization of the engineered structure was performed to allow the system to remediate the bad geometry and to relax from its lattice-constrained conformation.

Publication Year: 2012

Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling.

(2012) J Cell Biol 199

PubMed: 23027905 | PubMedCentral: PMC3461504 | DOI: 10.1083/jcb.201204010

1JFF ; Li et al., 2002 ) was performed in the University of California, San Francisco Chimera with the fit model in map function ( Pettersen et al., 2004 ).

Publication Year: 2012

Rationalization of paclitaxel insensitivity of yeast ?-tubulin and human ?III-tubulin isotype using principal component analysis.

(2012) BMC Res Notes 5

PubMed: 22849332 | PubMedCentral: PMC3477043 | DOI: 10.1186/1756-0500-5-395

A total of 22 tubulin residues, occurring within 5 Å from paclitaxel in the paclitaxel-bound tubulin structure (pdb code: 1JFF) [ 23 ], were identified and defined as the paclitaxel bi... ding site (PBS) residues.

a) Disposition of Val23, Asp26 and paclitaxel in paclitaxel-bound β-tubulin (pdb ID:1JFF).

Figure 6 Disposition of a) paclitaxel, Phe272 and His229, and b) paclitaxel, Lys19 and Glu22 in paclitaxel-bound β-tubulin (pdb ID: 1JFF).

From a multiple sequence alignment using the program ClustalW [ 24 ], amino acids corresponding to the 22 PBS residues were identified in 125 eukaryotic β-tubulin sequences, as shown in Figure  1 (through out this work we have used sequence numbering used in the PDB entry 1JFF; this sequence numbering is slightly different from the original sequence numbering to accommodate sequence alignment of α and β–chains).

The rotameric state of Val23 in the original pdb file (1JFF) was maintained during the mutation.

The structures for paclitaxel-bound (PDB ID: 1JFF) [ 23 ] and paclitaxel-free (PDB ID: 1SA0) [ 34 ] tubulin were downloaded from the protein data bank [ 35 ].

Sequence numbering is consistent with that used in the pdb file 1JFF.

Figure 5 Loop-loop interactions in paclitaxel-bound animal β-tubulin (pdb ID: 1JFF).

As shown in Figure  4 d, Lys19, Phe20, Val23, and Asp26 β-tubulin is part of a helix in paclitaxel-bound (pdb code: 1JFF) as well as in paclitaxel-free (pdb code: 1SA0) structure.

Figure 4 Paclitaxel-bound (pdb ID:1JFF) and paclitaxel-free (pdb ID: 1SA0) β-tubulin.

Upon paclitaxel binding (pdb ID: 1JFF) this loop becomes ordered.

d) An α-helix in β-tubulin (containing residues 19, 20 and 23) as found in two crystal structures: 1SA0 (paclitaxel-free) and 1JFF (paclitaxel-bound).

a) The side-chain of Ser277 is shown in two rotameric states — the first rotamer (as found in 1JFF) lacks Ser277-Lys218 interaction while the second rotamer (generated in silico ) shows Ser277-Lys218 H-bond (blue line) interaction.

Publication Year: 2012

Multimodal microtubule binding by the Ndc80 kinetochore complex.

(2012) Nat Struct Mol Biol 19

PubMed: 23085714 | PubMedCentral: PMC3492541 | DOI: 10.1038/nsmb.2411

Figure 5 Structural analysis of the Ndc80c–microtubule interface ( a ) Crystal structures of two bonsai Δ1–80 molecules (PDB 2VE7) and tubulin (PDB 1JFF) docked into the improv... d cryo-EM density map, colored as in Fig. 1a .

All rigid-body docking of protein crystal structures (tubulin: 1JFF 57 , Ndc80 bonsai: 2VE7 18 ), and preparation of molecular graphics illustrations was performed with UCSF Chimera 58 .

Publication Year: 2012

Kar3Vik1 uses a minus-end directed powerstroke for movement along microtubules.

(2013) PLoS One 8

PubMed: 23342004 | PubMedCentral: PMC3544905 | DOI: 10.1371/journal.pone.0053792

To further analyze the Kar3Vik1 stalk rotation in molecular detail we docked the X-ray crystal structure of Kar3Vik1 (PDB accession: 4ETP, [6] ) and the αβ-tubulin dimer (PDB accession... 1JFF, [33] ) into the 3-D density maps obtained from helical reconstruction.

This model is proposed based on the structural changes seen in helical reconstructions ( Fig. 3 ) and X-ray crystal structure docking into the density maps obtained from helical averaging (αβ-tubulin, PDB accession: 1JFF, [33] ; Kar3Vik1, PDB accession: 4ETP, [6] ).

The crystal structure of the αβ-tubulin dimer (PDB accession: 1JFF) [33] and the X-ray crystal structure of the ADP-state Kar3Vik1 heterodimer (SHD-Kar3Vik1E355C-K423C –EBI, PDB accession: 4ETP) [6] were docked manually into the density maps using UCSF Chimera.

( C & D ) The X-ray crystal structures of tubulin (PDB accession: 1JFF; [33] ) and Kar3Vik1 (PDB accession: 4ETP; [6] ) docked into the scaffolds of Nanogold®-labeled GCN4-Kar3CFVik1C536C helical averages in the nucleotide-free ( C ) and AMPPNP states ( D ).

Publication Year: 2013

Comparison of Epothilone and Taxol Binding in Yeast Tubulin using Molecular Modeling.

(2011) Avicenna J Med Biotechnol 3

PubMed: 23407671 | PubMedCentral: PMC3558196 | DOI: null

A) Taxol as found in the electron crystallography model (PDB: 1JFF).

Known 3D structure of proteins Three-dimensional protein structures of bovine brain tubulin in complex with taxol (1JFF) and epothiloneA (1TVK) were obtained from the Protein Data Bank (PDB) [ http// ] ( 14 , 15 ).

Molecular modeling visualization and analysis Modeled yeast tubulin was superimposed with PyMol on the bovine β-tubulin in complex with taxol (1JFF) for comparison of three-dimensional structure of two proteins.

Structural presentation of 1JFF and 1TVK and modeled yeast tubulin was made by using Swiss-Pdb Viewer and PyMOL (Version 0.99) [ ] programs ( 21 ).

Publication Year: 2011

Structural basis of tubulin tyrosination by tubulin tyrosine ligase.

(2013) J Cell Biol 200

PubMed: 23358242 | PubMedCentral: PMC3563685 | DOI: 10.1083/jcb.201211017

1JFF ( Löwe et al., 2001 ).

Publication Year: 2013

Determination of the optimal tubulin isotype target as a method for the development of individualized cancer chemotherapy.

(2013) Theor Biol Med Model 10

PubMed: 23634782 | PubMedCentral: PMC3651705 | DOI: 10.1186/1742-4682-10-29

The paclitaxel complex is based on PDB:1JFF, the colchicine complex is based on PDB:1SA0, and the vinblastine complex is based on PDB:1Z2B.

Publication Year: 2013

Structure of the tubulin/FtsZ-like protein TubZ from Pseudomonas bacteriophage ?KZ.

(2013) J Mol Biol 425

PubMed: 23528827 | PubMedCentral: PMC3678025 | DOI: 10.1016/j.jmb.2013.03.019

ΦKZ TubZ forms canonical protofilaments with a competent GTPase site ΦKZ TubZ formed crystallographic protofilaments with a subunit–subunit interface essentially identical with... that resolved for tubulin [Protein Data Bank (PDB) ID: 1JFF ] and FtsZ (PDB ID: 4DXD ).

24 (b) Structural superimposition of the protofilament crystal structures of ΦKZ TubZ and tubulin (PDB ID: 1JFF ).

Whereas the catalytic aspartate within loop T7 of 201Φ2-1 TubZ (PhuZ) is found 12.2 Å from the β-phosphate of GDP, too long a distance for efficient nucleotide hydrolysis, in protofilaments of tubulin (PDB ID: 1JFF ) and FtsZ (PDB ID: 4DXD ), this distance is 5.7 Å and 7.1 Å, respectively.

Whereas 201Φ2-1 TubZ (PhuZ) has an extremely small longitudinal surface contact (188 Å 2 buried by both contributing subunits excluding the C-terminal tail), the ΦKZ interface encompasses 986 Å 2 (buried by both contributing subunits excluding the C-terminal tail), a comparable figure to that of tubulin and FtsZ protofilaments (PDB IDs 1JFF and 4DXD1JFF4DXD bury 1666 and 1151 Å 2 , respectively).

Publication Year: 2013

NMK-TD-100, a novel microtubule modulating agent, blocks mitosis and induces apoptosis in HeLa cells by binding to tubulin.

(2013) PLoS One 8

PubMed: 24116100 | PubMedCentral: PMC3792137 | DOI: 10.1371/journal.pone.0076286

Molecular Modeling of NMK-TD-100-Tubulin Binding The crystal structure of αβ-tubulin (PDB ID: 1JFF) was utilized as template for docking studies [ 41 ].

and it was found the binding energy (-71.82 kcal/mol) is less negative compared with when docked to site 1 of pdb 1JFF.

The energy minimized structures of tubulin (1JFF.

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

For comparison with the taxol binding site, the structure of α/β-tubulin dimers bound to taxol was used (PDB 1JFF ) ( 44 ).

Publication Year: 2014

Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure.

(2014) Mol Biol Cell 25

PubMed: 24227885 | PubMedCentral: PMC3890346 | DOI: 10.1091/mbc.E13-07-0387

(A) End-on view of the deacetylated, dynamic microtubule reconstruction with the docked electron crystallographic structure of tubulin (1JFF).

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

g001 Figure 1 Conformational rearrangements of α- and β-subunits of the straight (PDB entry 1JFF [4] , resolution 3.5 Å) and bent (PDB entry 1SA0 [7] , resolution 3.58 Å... ) tubulin heterodimers.

Methods Preparation of endpoint structures of conformational landscapes Selection of straight and bent tubulin endpoint structures Conformational change coordinates for tubulin are bounded by the taxol-liganded straight tubulin heterodimer, observed in zinc-induced protofilament sheets (PDB id 1JFF, resolution 3.5 Å, organism B. taurus ), and the bent tubulin structure observed in the α 1 β 1 heterodimer of the T2R-colchicine complex (PDB id 1SA0, resolution 3.58 Å, organism B. taurus ) (see Figure S1 in Text S1 ).

Soluble GDP-tubulin was previously thought to exist in only two states, the “straight” and “bent” structures represented by PDB ids 1JFF and 1SA0, respectively.

Unpolymerized tubulin For the straight tubulin endpoint structure, taxol and the Zn 2+ ion were removed from 1JFF while preserving the Mg 2+ ion-coordinated GTP molecule on the N-site of the α-subunit and the GDP molecule on the E-site of the β-subunit.

Publication Year: 2014

An In silico Based Comparison of Drug Interactions in Wild and Mutant Human ?-tubulin through Docking Studies.

(2014) Avicenna J Med Biotechnol 6

PubMed: 24834310 | PubMedCentral: PMC4009099 | DOI: null

Out of the reported hits, 1JFF was downloaded from Protein Data Bank ( ) ( 40 ) which was further considered as a template (1JFF-B chain) for the modeling of the query sequence.

Figure 1 Pairwise sequence alignment of template (1JFF-B chain) with the query sequence of human β-tubulin Figure 2 3D structure of the template; A) the modelled structure of human β-tubulin; B) and its structural superimposition C) Conversely, chemical compounds needed for docking against wild and the mutants of human β-tubulin were obtained from marine flora.

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4020581

Table 3 Amino Acid Residues of β-Tubulin Lying within 4 Å of Paclitaxel and Residues of Bs FtsZ Lying within 4 Å of the Paclitaxel-like Site a β-tubulin (PDB entry 1JFF... Bs FtsZ (PDB entry 2RHL) Glu22 Arg29 Val23 Glu32 Asp25 Asn33 Glu26 Glu185 Leu217 Asn188 Asp226 Arg191 His229 Gln195 Leu230 Ile230 Ala233 Asn301 Ser236 Glu305 Phe272   Pro274   Leu275   Thr276   Ser277   Arg278   Pro368   Arg369   Gly370   a The residues of Bs FtsZ close to paclitaxel-like site projected to be bound by docked PC190723 and SB-RA-2001 are shown in bold.

The β-tubulin with GDP and paclitaxel was extracted from tubulin of Bos taurus (PDB entry 1JFF).

In this respect, the crystal structures of tubulin (PDB entry 1JFF) and Bs FtsZ (PDB entry 2RHL) were superimposed on each other and structurally aligned using PyMol to determine the residues of Bs FtsZ that were in the proximity of the paclitaxel binding site in tubulin.

Publication Year: 2014

Regulation of microtubule motors by tubulin isotypes and post-translational modifications.

(2014) Nat Cell Biol 16

PubMed: 24633327 | PubMedCentral: PMC4117587 | DOI: 10.1038/ncb2920

Tubulin and microtubule model generation For illustrative purpose a linear polypeptide chain of TUBA1A and TUBB2A CTTs were generated using Pymol program and fused to the last visible residue of alpha... and beta chains in the microtubule model (generated using PDB:1JFF) shown in Fig. 1a .

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4139185

41 The related rotational echo double resonance (REDOR)-taxol structure was proposed by Ojima in 2005 40 based on initial REDOR experiments reported in 2000 by Bane et al. 47 The structure was modifie... 48 by a second set of REDOR NMR data 49 and by modeling the structure in a reshaped 1JFF tubulin structure.

Figure 21 Comparison of interatomic distances (Å) for taxol and 7a with the same C13-side chain conformation: (a) taxol (pdf code 1JFF) with distances from the C13 phenyl ring centroids and C3′ to the oxetane oxygen; (b) compound 7a with similar distances to the spirocyclic oxetane oxygen.

Publication Year: 2014

A tethered delivery mechanism explains the catalytic action of a microtubule polymerase.

(2014) Elife 3

PubMed: 25097237 | PubMedCentral: PMC4145800 | DOI: 10.7554/eLife.03069

( E ) Structural superposition of TOG2-bound αβ-tubulin (colored) and the straight conformation of αβ-tubulin (PDB 1JFF, gray), showing the ∼13° rotatio... of β-tubulin relative to α-tubulin that is characteristic of the curved conformation.

Lowe J , Li H , Downing KH , Nogales E , 2001 , Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol , , Publicly available at RCSB Protein Data Bank.

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4226729

1JFF ) conformations of αβ-tubulin.

Curved and straight structures are PDB 4FFB and 1JFF , respectively.

1JFF ) and a partially straightened assembly (tan) from GMPCPP ribbons are shown for reference.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4298687

(B) Positions of charged residues targeted for alanine mutagenesis in the sequences of α- and β-tubulin from yeast S. cerevisiae (Sc), aligned with the corresponding sequences in pig S... scrofa (Ss) tubulin (PDB ID: 1JFF ; Löwe et al., 2001 ).

S4 B. The DireX program ( Wang and Schröder, 2012 ) was used for flexible fitting of the crystal structure of the dynein MTBD (PDB ID: 3KVH ; Kon et al., 2012 ) and tubulin dimer (PDB ID: 1JFF ; Löwe et al., 2001 ) into the map.

Note: In this paper, we adopted numbering of amino acid residues for S. cerevisiae yeast tubulin, which is slightly different from that of the Sus scrofa pig tubulin used in the PDB file 1JFF ( Fig. 1 B ).

Publication Year: 2015

PubMed ID is not available.

Published in 2011

PubMedCentral: PMC4412091

Also all designed structures as well as griseofulvin were docked into the active site of microtubule (1JFF), using Autodock program.

Because the griseofulvin binding site partially overlaps with the paclitaxel site in tubulin [ 30 ], therefore, microtubul complexed with paclitaxel (1JFF) was obtained from Protein Data Bank for docking studies.

Autodock program used and all designed structures as well as griseofulvin were docked into the active site of 1JFF.

Modeling All the compounds ( Table 2 ) as well as griseofulvin were docked into the active site of microtubule, which was obtained from Protein Data Bank (1JFF) using Autodock 4.2.

The microtubule complexed with paclitaxol was obtained from Protein Data Bank (1JFF).

Publication Year: 2011

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4436829

To obtain a short segment of the MT wall, we fitted the crystal structure of the tubulin dimer (1JFF.

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4460180

Computational Simulations Binding to the Taxane Binding Site The coordinates of the tubulin-taxane receptor-ligand complex were obtained from the PDB crystal structure 1JFF [ 34 ], which represents pa... litaxel co-crystallized with tubulin.

Next, the protonation state of ionizable residues in 1JFF was determined using PROPKA and hydrogen atoms added to obtain a complete αβ-tubulin heterodimer.

Publication Year: 2015