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(-) Description

Title :  STRUCTURAL BASIS OF TRANSCRIPTION ACTIVATION BY THE CYCLIN T1-TAT-TAR RNA COMPLEX FROM EIAV
 
Authors :  K. Anand, M. Geyer
Date :  30 Oct 08  (Deposition) - 09 Dec 08  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym. Unit :  A,B,C,D,R,S
Biol. Unit 1:  A,C,R  (1x)
Biol. Unit 2:  B,D,S  (1x)
Keywords :  Rna-Binding Protein, Tar, Tat, Cyclin, Nucleus, Activator, Cyclin T1, Host-Virus Interaction, Transcription Regulation, Cell Cycle, Rna-Binding, Acetylation, Coiled Coil, Transcription, Cell Division, Crystallization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Anand, A. Schulte, K. Vogel-Bachmayr, K. Scheffzek, M. Geyer
Structural Insights Into The Cyclin T1-Tat-Tar Rna Transcription Activation Complex From Eiav.
Nat. Struct. Mol. Biol. V. 15 1287 2008
PubMed-ID: 19029897  |  Reference-DOI: 10.1038/NSMB.1513

(-) Compounds

Molecule 1 - CYCLIN-T1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 5-267
    Organism Common: HORSE
    Organism Scientific: EQUUS CABALLUS
    Organism Taxid: 9796
    Other Details: GENBANK: AF137509
    Synonym: CYCT1, CYCLIN-T
 
Molecule 2 - PROTEIN TAT
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CYCLIN BOX DOMAIN OF EQUINE CYCLIN T1, RESIDUES 47-75
    Organism Scientific: EQUINE INFECTIOUS ANEMIA VIRUS
    Organism Taxid: 11665
    Strain: PGEX-4T1
    Synonym: CYCLIN T1-TAT FUSION PROTEIN, TRANSACTIVATING REGULATORY PROTEIN, ETAT, E-TAT
 
Molecule 3 - 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'
    Chains: R, S
    Organism Scientific: EQUINE INFECTIOUS ANEMIA VIRUS
    Organism Taxid: 11665
    Other Details: TAR RNA MOLECULES WERE TRANSCRIBED IN VITRO FROM SINGLE STRANDED ANTISENSE DNA OLIGONUCLEOTIDE USING T7 PROMOTER AND POLYMERASE SYSTEM.
    Other Details - Source: PURIFIED SINGLE-STRANDED DNA OLIGONUCLEOTIDES
    Synonym: TAR RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDRS
Biological Unit 1 (1x): A C R 
Biological Unit 2 (1x):  B D S

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (0, 0)

(no "Site" information available for 2W2H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W2H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:6 -Asn A:7
2Asn B:257 -Trp B:258
3Ala C:46 -Ser C:47
4Ala D:46 -Ser D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W2H)

(-) Exons   (0, 0)

(no "Exon" information available for 2W2H)

(-) Sequences/Alignments

Asymmetric 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:263
 aligned with CCNT1_HORSE | Q9XT26 from UniProtKB/Swiss-Prot  Length:727

    Alignment length:263
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   
          CCNT1_HORSE     5 RKNNNKRWYFTREQLENSPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHACLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIRNWRACQAAKKT 267
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.......hhhhhhh........hhhhh..hhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2h A   5 RKNNNKRWYFTREQLENSPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACQAAKKT 267
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with CCNT1_HORSE | Q9XT26 from UniProtKB/Swiss-Prot  Length:727

    Alignment length:260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
          CCNT1_HORSE     4 ERKNNNKRWYFTREQLENSPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHACLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIRNWRACQA 263
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Cyclin_N-2w2hB01 B:10-149                                                                                                                   ------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------Cyclin_N-2w2hB02 B:10-149                                                                                                                   ------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.......hhhhhhh........hhhhh..hhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2h B   4 QRKNNNKRWYFTREQLENSPSRRFGLDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTRFHRNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACQA 263
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263


Chain C from PDB  Type:PROTEIN  Length:29
 aligned with TAT_EIAVY | P20920 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:29
                                    56        66         
            TAT_EIAVY    47 IDYLDASLRKKNKQRLKAIQQGRQPQYLL  75
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 2w2h C  41 IDYLDASLRKKNKQRLKAIQQGRQPQYLL  69
                                    50        60         


Chain D from PDB  Type:PROTEIN  Length:29
 aligned with TAT_EIAVY | P20920 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:29
                                    56        66         
            TAT_EIAVY    47 IDYLDASLRKKNKQRLKAIQQGRQPQYLL  75
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
           Pfam domains (1) Tat-2w2hD01 D:41-59---------- Pfam domains (1)
           Pfam domains (2) Tat-2w2hD02 D:41-59---------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
                 Transcript ----------------------------- Transcript
                 2w2h D  41 IDYLDASLRKKNKQRLKAIQQGRQPQYLL  69
                                    50        60         


Chain R from PDB  Type:RNA  Length:22
                                                      
                 2w2h R   3 GCUCAGAUUCUGCGGUCUGAGC  24
                                    12        22  


Chain S from PDB  Type:RNA  Length:22
                                                      
                 2w2h S   3 GCUCAGAUUCUGCGGUCUGAGC  24
                                    12        22
   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  (0, 0)

(no "SCOP Domain" information available for 2W2H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W2H)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Cyclin (63)
(-)
Clan: no clan defined [family: Tat] (12)

(-) Gene Ontology  (24, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CCNT1_HORSE | Q9XT26)
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: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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0000307    cyclin-dependent protein kinase holoenzyme complex    Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
    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: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,D   (TAT_EIAVY | P20920)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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.

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 Related Entries

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