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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 TAT COMPLEXED WITH HUMAN P-TEFB
 
Authors :  T. H. Tahirov, N. D. Babayeva, K. Varzavand, J. J. Cooper, S. C. Sedore, D
Date :  09 Apr 10  (Deposition) - 09 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  P-Tefb, Tat, Hiv-1, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. H. Tahirov, N. D. Babayeva, K. Varzavand, J. J. Cooper, S. C. Sedore, D. H. Price
Crystal Structure Of Hiv-1 Tat Complexed With Human P-Tefb.
Nature V. 465 747 2010
PubMed-ID: 20535204  |  Reference-DOI: 10.1038/NATURE09131

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN KINASE 9
    ChainsA
    EC Number2.7.11.22, 2.7.11.23
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineBL21 INSECT CELLS
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPENTR/SD/D-TOPO VECTOR (INVITROGEN K2420)
    Expression System StrainSF9
    Expression System Vector TypeBACULO VIRUS
    FragmentUNP RESIDUES 1-345, PROTEIN KINASE DOMAIN
    GeneCDC2L4, CDK9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYCLIN-DEPENDENT KINASE 9, SERINE/THREONINE-PROTEIN KINASE PITALRE, CELL DIVISION CYCLE 2-LIKE PROTEIN KINASE 4, C-2K
 
Molecule 2 - CYCLIN-T1
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineBL21 INSECT CELLS
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPENTR/SD/D-TOPO VECTOR (INVITROGEN K2420)
    Expression System StrainSF9
    Expression System Vector TypeBACULO VIRUS
    FragmentUNP RESIDUES 1-266
    GeneCCNT1, CYCLIN T1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYCLIN-T, CYCT1
 
Molecule 3 - PROTEIN TAT
    ChainsC
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineBL21 INSECT CELLS
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPENTR/SD/D-TOPO VECTOR (INVITROGEN K2420)
    Expression System StrainSF9
    Expression System Vector TypeBACULO VIRUS
    GeneTAT
    Organism CommonHIV-1
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid11706
    StrainISOLATE HXB2 GROUP M SUBTYPE B
    SynonymTRANSACTIVATING REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1TPO1Mod. Amino AcidPHOSPHOTHREONINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:22 , HIS C:33 , CYS C:34 , CYS C:37BINDING SITE FOR RESIDUE ZN C 87
2AC2SOFTWARECYS B:261 , CYS C:25 , CYS C:27 , CYS C:30BINDING SITE FOR RESIDUE ZN C 88

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MI9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:318 -Pro A:319

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041982F59LCDK9_HUMANPolymorphism55640715AF59L
2UniProtVAR_013456G231ACDK9_HUMANPolymorphism  ---AG231A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDK9_HUMAN25-48  1A:25-48
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDK9_HUMAN145-157  1A:145-157

(-) Exons   (15, 15)

Asymmetric/Biological Unit (15, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002619001ENSE00001164718chr12:49110781-49110298484CCNT1_HUMAN1-54541B:7-5448
1.2ENST000002619002ENSE00000914192chr12:49108307-4910822682CCNT1_HUMAN54-81281B:54-8128
1.3ENST000002619003ENSE00000938798chr12:49099679-49099551129CCNT1_HUMAN82-124431B:82-12443
1.4ENST000002619004ENSE00000938799chr12:49094856-4909479661CCNT1_HUMAN125-145211B:125-14521
1.5ENST000002619005ENSE00000938800chr12:49093623-4909356163CCNT1_HUMAN145-166221B:145-16622
1.6ENST000002619006ENSE00000938801chr12:49091966-4909192146CCNT1_HUMAN166-181161B:166-18116
1.8ENST000002619008ENSE00000938802chr12:49089945-49089782164CCNT1_HUMAN181-236561B:181-23656
1.9ENST000002619009ENSE00000938803chr12:49089612-4908954271CCNT1_HUMAN236-259241B:236-25217
1.10ENST0000026190010ENSE00001164708chr12:49088219-490867521468CCNT1_HUMAN260-7264670--

2.1cENST000003732641cENSE00001251705chr9:130548328-130548519192CDK9_HUMAN1-31311A:8-3124
2.2aENST000003732642aENSE00000984615chr9:130548980-13054906182CDK9_HUMAN31-58281A:31-5828
2.3cENST000003732643cENSE00000984616chr9:130549797-13054988791CDK9_HUMAN59-89311A:59-8830
2.4ENST000003732644ENSE00000984617chr9:130550226-130550392167CDK9_HUMAN89-144561A:97-14448
2.5bENST000003732645bENSE00000984618chr9:130550493-130550664172CDK9_HUMAN145-202581A:145-20258
2.6cENST000003732646cENSE00000984619chr9:130550823-130550971149CDK9_HUMAN202-251501A:202-25150
2.7cENST000003732647cENSE00001814236chr9:130551457-1305530661610CDK9_HUMAN252-3721211A:252-34493

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:329
 aligned with CDK9_HUMAN | P50750 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:337
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       
           CDK9_HUMAN     8 VECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHLTSMFEYLAPPRR 344
               SCOP domains d3mi9a_ A: Cell division protein kinase 9, CDK9                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Pkinase-3mi9A01 A:19-315                                                                                                                                                                                                                                                                                 ----------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeee........eeeeee.....eeeeee..........hhhhhhhhhhhhhh.......eeeeeee.--------.eeeeeee...eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.................hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh......hhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1c  PDB: A:8-31  ---------------------------Exon 2.3c  PDB: A:59-88        -------------------------------------------------------Exon 2.5b  PDB: A:145-202 UniProt: 145-202                -------------------------------------------------Exon 2.7c  PDB: A:252-344 UniProt: 252-372 [INCOMPLETE]                                       Transcript 2 (1)
           Transcript 2 (2) -----------------------Exon 2.2a  PDB: A:31-58     ------------------------------Exon 2.4  PDB: A:97-144 UniProt: 89-144 [INCOMPLETE]    ---------------------------------------------------------Exon 2.6c  PDB: A:202-251 UniProt: 202-251        --------------------------------------------------------------------------------------------- Transcript 2 (2)
                 3mi9 A   8 VECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTK--------GSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYtNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHLTSMFEYLAPPRR 344
                                    17        27        37        47        57        67        77        87|       97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       
                                                                                                           88       97                                                                                      186-TPO                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with CCNT1_HUMAN | O60563 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:255
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
          CCNT1_HUMAN     7 NNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRAC 261
               SCOP domains d3mi9b1 B:7-150 automated matches                                                                                                               d3mi9b2 B:151-261 automated matches                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Cyclin_N-3mi9B01 B:9-149                                                                                                                     ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh--------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:7-54 UniProt: 1-54 [INCOMPLETE]---------------------------Exon 1.3  PDB: B:82-124 UniProt: 82-124    Exon 1.4             --------------------Exon 1.6        ------------------------------------------------------Exon 1.9  PDB: B:236-2521. Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.2  PDB: B:54-81      ---------------------------------------------------------------Exon 1.5              --------------Exon 1.8  PDB: B:181-236 UniProt: 181-236               ------------------------- Transcript 1 (2)
                 3mi9 B   7 NNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRL--------C 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246     |   -    |
                                                                                                                                                                                                                                                                               252      261

Chain C from PDB  Type:PROTEIN  Length:49
 aligned with TAT_HV1H2 | P04608 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:49
                                    10        20        30        40         
            TAT_HV1H2     1 MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGR  49
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains Tat-3mi9C01 C:1-49                                Pfam domains
         Sec.struct. author ........hhhhh...............hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3mi9 C   1 MEPVDPRLEPWKHPGSQPKTACTNCYCKKCCFHCQVCFITKALGISYGR  49
                                    10        20        30        40         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MI9)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Cyclin (63)
(-)
Clan: PKinase (934)

(-) Gene Ontology  (74, 99)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDK9_HUMAN | P50750)
molecular function
    GO:0097322    7SK snRNA binding    Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008353    RNA polymerase II carboxy-terminal domain kinase activity    Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
    GO:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004693    cyclin-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    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.
    GO:0005515    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).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
    GO:0001223    transcription coactivator binding    Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0016740    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.
biological process
    GO:0006281    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.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    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.
    GO:0071345    cellular response to cytokine 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 cytokine stimulus.
    GO:0071157    negative regulation of cell cycle arrest    Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:1900364    negative regulation of mRNA polyadenylation    Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
    GO:0016310    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.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:2001168    positive regulation of histone H2B ubiquitination    Any process that activates or increases the frequency, rate or extent of histone H2B ubiquitination.
    GO:0033129    positive regulation of histone phosphorylation    Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.
    GO:1903839    positive regulation of mRNA 3'-UTR binding    Any process that activates or increases the frequency, rate or extent of mRNA 3'-UTR binding.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006282    regulation of DNA repair    Any process that modulates the frequency, rate or extent of DNA repair.
    GO:0031056    regulation of histone modification    Any process that modulates the frequency, rate or extent of the covalent alteration of a histone.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0051147    regulation of muscle cell differentiation    Any process that modulates the frequency, rate or extent of muscle cell differentiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0042795    snRNA transcription from RNA polymerase II promoter    The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016605    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.
    GO:0008024    cyclin/CDK positive transcription elongation factor complex    A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    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.
    GO:0008023    transcription elongation factor complex    Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.

Chain B   (CCNT1_HUMAN | O60563)
molecular function
    GO:0097322    7SK snRNA binding    Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA).
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0016538    cyclin-dependent protein serine/threonine kinase regulator activity    Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other proteins.
    GO:0005515    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).
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:1900364    negative regulation of mRNA polyadenylation    Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
    GO:0045737    positive regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that activates or increases the frequency, rate or extent of CDK activity.
    GO:1901409    positive regulation of phosphorylation of RNA polymerase II C-terminal domain    Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042795    snRNA transcription from RNA polymerase II promoter    The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    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.
cellular component
    GO:0008024    cyclin/CDK positive transcription elongation factor complex    A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    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.

Chain C   (TAT_HV1H2 | P04608)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042805    actinin binding    Interacting selectively and non-covalently with actinin, any member of a family of proteins that crosslink F-actin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    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).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0030683    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.
    GO:0039586    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.
    GO:0039525    modulation by virus of host chromatin organization    Any process in which a virus effects a change in the organization of chromatin in the host.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0039503    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.
    GO:0039502    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    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.
cellular component
    GO:0005576    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.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044196    host cell nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic host cells.
    GO:0042025    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.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CCNT1_HUMAN | O605632pk2 3blh 3blq 3blr 3lq5 3mia 3my1 3tn8 3tnh 3tni 4bcf 4bcg 4bch 4bci 4bcj 4ec8 4ec9 4imy 4ogr 4or5 5l1z
        CDK9_HUMAN | P507501pf6 3blh 3blq 3blr 3lq5 3mia 3my1 3tn8 3tnh 3tni 4bcf 4bcg 4bch 4bci 4bcj 4ec8 4ec9 4imy 4ogr 4or5 5l1z
        TAT_HV1H2 | P046083mia 4or5

(-) Related Entries Specified in the PDB File

3mia