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Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb
Biology and Chemistry Report
3MIA
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN BINDING
    Text P-TEFb, Cdk9, Cyclin T1, HIV-1, Tat, PROTEIN BINDING

    Polymeric Molecules

    Chain A
    Description Cell division protein kinase 9 
    Fragment UNP residues 1-345, Protein kinase domain 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 40692.6 
    Source Method genetically manipulated  
    Entity Name Cyclin-dependent kinase 9, Serine/threonine-protein kinase PITALRE, Cell division cycle 2-like protein kinase 4, C-2K 
    Chain B
    Description Cyclin-T1 
    Fragment UNP residues 1-266 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 30877.5 
    Source Method genetically manipulated  
    Entity Name Cyclin-T, CycT1 
    Chain C
    Description Protein Tat 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 9848.4 
    Source Method genetically manipulated  
    Entity Name Transactivating regulatory protein 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ANP  PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER  C10 H17 N6 O12 P3   506.20  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A CDK9_HUMAN P50750     
    B CCNT1_HUMAN A9XU13     
    C TAT_HV1H2 O09778     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.11.22      
    2.7.11.23      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    6974   Cellular Response to DNA Damage Stimulus  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 a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    16310   Phosphorylation  The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 
    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. 
    16605   Pml Body  A Class of Nuclear Body; They React Against Sp100 Auto Antibodies (pml Promyelocytic Leukemia); Cells Typically Contain 10 30 Pml Bodies Per Nucleus; Alterations in the Localization of Pml Bodies Occurs After Viral Infection. 
    4674   Protein Serine/threonine Kinase Activity  Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    Chain C
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    30683   Evasion or Tolerance by Virus of Host Immune Response  Any Process Either Active or Passive by Which a Virus Avoids the Effects of the Host Organism's Immune Response. the Host Is Defined As the Larger of the Organisms Involved in a Symbiotic Interaction. 
    39502   Suppression by Virus of Host Type I Interferon Mediated Signaling Pathway  Any Process in Which a Virus Stops Prevents or Reduces the Frequency Rate or Extent of Type I Interferon Mediated Signaling in the Host Organism. Type I Interferons Include the Interferon Alpha Beta Delta Episilon Zeta Kappa Tau and Omega Gene Families. 
    39503   Suppression by Virus of Host Innate Immune Response  Any Process in Which a Virus Stops Prevents or Reduces the Frequency Rate or Extent of the Innate Immune Response of the Host Organism the Host's First Line of Defense. 
    39525   Modulation by Virus of Host Chromatin Organization  Any Process in Which a Virus Effects a Change in the Organization of Chromatin in the Host. 
    39586   Modulation by Virus of Host Pp1 Activity  The Process in Which a Virus Effects a Change in Host Protein Phosphatase 1 (pp1) Activity a Serine/threonine Phosphatase. Different Viruses Modulate Host Pp1 Activity to Remove Phosphates From Various Cellular Substrates and Downregulate the Host's Antiviral Response. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    30430   Host Cell Cytoplasm  The Cytoplasm of a Host Cell. 
    42025   Host Cell Nucleus  A Membrane Bounded Organelle As It Is Found in the Host Cell in Which Chromosomes Are Housed and Replicated. the Host Is Defined As the Larger of the Organisms Involved in a Symbiotic Interaction. 
    44196   Host Cell Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Host Cells. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    42805   Actinin Binding  Interacting Selectively and Non Covalently with Actinin Any Member of a Family of Proteins That Crosslink F Actin. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C
    Common Name Hiv 1
    Scientific Name Human immunodeficiency virus type 1  
    Strain ISOLATE HXB2 GROUP M SUBTYPE B
    Gene tat
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Type Insect Cells
    Host Strain Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name pENTR/SD/D-TOPO vector (Invitrogen K2420)


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ccnt1, cyclin t1
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Type Insect Cells
    Host Strain Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name pENTR/SD/D-TOPO vector (Invitrogen K2420)


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cdc2l4, cdk9
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Type Insect Cells
    Host Strain Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name pENTR/SD/D-TOPO vector (Invitrogen K2420)


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    9 9q34.1 1025     cyclin-dependent kinase 9 CDK9    
    12 12q13.11 904     cyclin T1 CCNT1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs146765767 LS-SNP   dbSNP   A 24 K - > R Beta Ladder 45% (Exposed) 9 130548498
    rs149950953 LS-SNP   dbSNP   A 58 G - > W Bend 10% (Intermediate) 9 130549059
    rs55640715 LS-SNP   dbSNP   A 59 F - > L Bend 3% (Buried) 9 130549799
    rs141709101 LS-SNP   dbSNP   A 87 T - > I Beta Ladder 35% (Intermediate) 9 130549882
    rs147073375 LS-SNP   dbSNP   A 108 H - > R Beta Ladder 13% (Intermediate) 9 130550283
    rs148342102 LS-SNP   dbSNP   A 193 W - > R 3/10 Helix 42% (Exposed) 9 130550637
    rs141577691 LS-SNP   dbSNP   A 233 T - > M Bend 49% (Exposed) 9 130550916
    rs11554104 LS-SNP   dbSNP   A 239 A - > T Helix 12% (Intermediate) 9 130550933
    rs145977259 LS-SNP   dbSNP   A 298 L - > P Bend 4% (Buried) 9 130551596
    rs139856271 LS-SNP   dbSNP   A 304 I - > M Coil 15% (Intermediate) 9 130551615
    rs201190553 LS-SNP   dbSNP   B 36 S - > P Helix 38% (Exposed) 12 49110353
    rs147254693 LS-SNP   dbSNP   B 71 M - > T Turn 10% (Intermediate) 12 49108257
    rs201367358 LS-SNP   dbSNP   B 218 G - > R Bend 57% (Exposed) 12 49089836
    rs35965578 LS-SNP   dbSNP   B 227 A - > P Bend 90% (Exposed) 12 49089809
    rs11834413 LS-SNP   dbSNP   B 235 D - > N Helix 38% (Exposed) 12 49089785
    rs147384648 LS-SNP   dbSNP   B 241 F - > L Helix 0% (Buried) 12 49089596