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Crystal structure of tubulin-RB3-TTL-Zampanolide complex
Biology and Chemistry Report
4I4T
  •   Structure Details   Hide

    Structure Keywords

    Keywords CELL CYCLE
    Text Alpha-tubulin, beta-tubulin, ligase, GTPase, stathmin, zamanolide, CELL CYCLE

    Polymeric Molecules

    Chain A,C
    Description Tubulin alpha-1B chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 50041.7 
    Source Method natural source  
    Entity Name Alpha-tubulin ubiquitous, Tubulin K-alpha-1, Tubulin alpha-ubiquitous chain 
    Chain B,D
    Description Tubulin beta-2B chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 50000.3 
    Source Method natural source  
    Chain E
    Description Stathmin-4 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 16844.3 
    Source Method genetically manipulated  
    Entity Name Stathmin-like protein B3, RB3 
    Chain F
    Description Tubulin Tyrosine ligase, TTL 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 44379.0 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ACP  PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER  C11 H18 N5 O12 P3   505.21  View 
    CA  CALCIUM ION  Ca   40.08  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    GDP  GUANOSINE-5'-DIPHOSPHATE  C10 H15 N5 O11 P2   443.20  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    GTP  GUANOSINE-5'-TRIPHOSPHATE  C10 H16 N5 O14 P3   523.18  View 
    MES  2-(N-MORPHOLINO)-ETHANESULFONIC ACID  C6 H13 N O4 S   195.24  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    TYR  TYROSINE  C9 H11 N O3   181.19  View 
    ZPN  (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide  C29 H39 N O6   497.62  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C TBA1B_BOVIN A6H700     
    B,D TBB2B_BOVIN Q6B856     
    E STMN4_RAT O35414     
    F E1BQ43_CHICK E1BQ43     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    226   Microtubule Cytoskeleton Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures Comprising Microtubules and Their Associated Proteins. 
    6184   GTP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    7017   Microtubule Based Process  Any Cellular Process That Depends Upon or Alters the Microtubule Cytoskeleton That Part of the Cytoskeleton Comprising Microtubules and Their Associated Proteins. 
    51258   Protein Polymerization  The Process of Creating Protein Polymers Compounds Composed of a Large Number of Component Monomers; Polymeric Proteins May Be Made Up of Different or Identical Monomers. Polymerization Occurs by the Addition of Extra Monomers to an Existing Poly or Oligomeric Protein. 
    71353   Cellular Response to Interleukin 4  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Interleukin 4 Stimulus. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5856   Cytoskeleton  Any of the Various Filamentous Elements That Form the Internal Framework of Cells and Typically Remain After Treatment of the Cells with Mild Detergent to Remove Membrane Constituents and Soluble Components of the Cytoplasm. the Term Embraces Intermediate Filaments Microfilaments Microtubules the Microtrabecular Lattice and Other Structures Characterized by a Polymeric Filamentous Nature and Long Range Order Within the Cell. the Various Elements of the Cytoskeleton Not Only Serve in the Maintenance of Cellular Shape But Also Have Roles in Other Cellular Functions Including Cellular Movement Cell Division Endocytosis and Movement of Organelles. 
    5874   Microtubule  Any of the Long Generally Straight Hollow Tubes of Internal Diameter 12 15 Nm and External Diameter 24 Nm Found in a Wide Variety of Eukaryotic Cells; Each Consists (usually) of 13 Protofilaments of Polymeric Tubulin Staggered in Such a Manner That the Tubulin Monomers Are Arranged in a Helical Pattern On the Microtubular Surface and with the Alpha/beta Axes of the Tubulin Subunits Parallel to the Long Axis of the Tubule; Exist in Equilibrium with Pool of Tubulin Monomers and Can Be Rapidly Assembled or Disassembled in Response to Physiological Stimuli; Concerned with Force Generation E.g. in the Spindle. 
    5881   Cytoplasmic Microtubule  Any Microtubule in the Cytoplasm of a Cell. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3725   Double Stranded RNA Binding  Interacting Selectively and Non Covalently with Double Stranded Rna. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5200   Structural Constituent of Cytoskeleton  The Action of a Molecule That Contributes to the Structural Integrity of a Cytoskeletal Structure. 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    1764   Neuron Migration  The Characteristic Movement of an Immature Neuron From Germinal Zones to Specific Positions Where They Will Reside As They Mature. 
    6184   GTP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    7017   Microtubule Based Process  Any Cellular Process That Depends Upon or Alters the Microtubule Cytoskeleton That Part of the Cytoskeleton Comprising Microtubules and Their Associated Proteins. 
    51258   Protein Polymerization  The Process of Creating Protein Polymers Compounds Composed of a Large Number of Component Monomers; Polymeric Proteins May Be Made Up of Different or Identical Monomers. Polymerization Occurs by the Addition of Extra Monomers to an Existing Poly or Oligomeric Protein. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5856   Cytoskeleton  Any of the Various Filamentous Elements That Form the Internal Framework of Cells and Typically Remain After Treatment of the Cells with Mild Detergent to Remove Membrane Constituents and Soluble Components of the Cytoplasm. the Term Embraces Intermediate Filaments Microfilaments Microtubules the Microtrabecular Lattice and Other Structures Characterized by a Polymeric Filamentous Nature and Long Range Order Within the Cell. the Various Elements of the Cytoskeleton Not Only Serve in the Maintenance of Cellular Shape But Also Have Roles in Other Cellular Functions Including Cellular Movement Cell Division Endocytosis and Movement of Organelles. 
    5874   Microtubule  Any of the Long Generally Straight Hollow Tubes of Internal Diameter 12 15 Nm and External Diameter 24 Nm Found in a Wide Variety of Eukaryotic Cells; Each Consists (usually) of 13 Protofilaments of Polymeric Tubulin Staggered in Such a Manner That the Tubulin Monomers Are Arranged in a Helical Pattern On the Microtubular Surface and with the Alpha/beta Axes of the Tubulin Subunits Parallel to the Long Axis of the Tubule; Exist in Equilibrium with Pool of Tubulin Monomers and Can Be Rapidly Assembled or Disassembled in Response to Physiological Stimuli; Concerned with Force Generation E.g. in the Spindle. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5200   Structural Constituent of Cytoskeleton  The Action of a Molecule That Contributes to the Structural Integrity of a Cytoskeletal Structure. 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    Chain E
    GO ID   Ontology GO Term Definition
    31110   Regulation of Microtubule Polymerization or Depolymerization  Any Process That Modulates the Frequency Rate or Extent of Microtubule Polymerization or Depolymerization by the Addition or Removal of Tubulin Heterodimers From a Microtubule. 
    Chain F
    GO ID   Ontology GO Term Definition
    226   Microtubule Cytoskeleton Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures Comprising Microtubules and Their Associated Proteins. 
    6464   Cellular Protein Modification Process  The Covalent Alteration of One or More Amino Acids Occurring in Proteins Peptides and Nascent Polypeptides (co Translational Post Translational Modifications) Occurring At the Level of an Individual Cell. Includes the Modification of Charged Trnas That Are Destined to Occur in a Protein (pre Translation Modification). 
    30516   Regulation of Axon Extension  Any Process That Modulates the Rate Direction or Extent of Axon Extension. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    4835   Tubulin Tyrosine Ligase Activity  Catalysis of the Reaction: ATP + Detyrosinated Alpha Tubulin + L Tyrosine = Alpha Tubulin + Adp + Phosphate. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Natural Source

    Chain B,D
    Common Name Bovine Cow Domestic Cattle Domestic Cow
    Scientific Name Bos taurus  
    Organ Brain
    Chain A,C
    Common Name Bovine Cow Domestic Cattle Domestic Cow
    Scientific Name Bos taurus  
    Organ Brain

    Genetic Source

    Chain F
    Common Name Bantam Chickens
    Scientific Name Gallus gallus  
    Gene ttl
    Host Scientific Name Escherichia coli  


    Chain E
    Common Name Brown Rat Rat Rats
    Scientific Name Rattus norvegicus  
    Gene stmn4
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 - 404053     tubulin, alpha 1a TUBA1A    
    15 15p12 79423     stathmin-like 4 STMN4    
    23 - 281555     tubulin, beta 2B class IIb TUBB2B