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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TANDEM BROMODOMAINS OF HUMAN TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1 (TAF1)
 
Authors :  P. Filippakopoulos, I. Felletar, S. Picaud, T. Keates, J. Muniz, O. Gil F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, Structural Genomics Consortium (Sgc)
Date :  29 Nov 11  (Deposition) - 18 Jan 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A
Keywords :  Tandem Bromodomain, Taf1, Cell Cycle Gene 1 Protein, Tbp-Associated Factor 250 Kda, Transcription Initiation Factor Tfiid 250 Kda Subunit, Tfii-250, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331  |  Reference-DOI: 10.1016/J.CELL.2012.02.013

(-) Compounds

Molecule 1 - TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1373-1635
    GeneBA2R, CCG1, CCGS, TAF1, TAF2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELL CYCLE GENE 1 PROTEIN, TBP-ASSOCIATED FACTOR 250 KDA, P250, TRANSCRIPTION INITIATION FACTOR TFIID 250 KDA SUBUNIT, TAF(II) 250, TAFII-250, TAFII250

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:98 , HOH A:115 , ARG A:1575 , SER A:1608 , GLN A:1609BINDING SITE FOR RESIDUE TRS A 1

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1640 -A:1640

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048433V1383ITAF1_HUMANPolymorphism7050748AV1404I
2UniProtVAR_076399R1431HTAF1_HUMANUnclassified (MRXS33)  ---AR1452H
3UniProtVAR_076400N1496HTAF1_HUMANUnclassified (MRXS33)  ---AN1517H

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.TAF1_HUMAN1397-1467
1520-1590
  2A:1418-1488
A:1541-1611
2BROMODOMAIN_1PS00633 Bromodomain signature.TAF1_HUMAN1402-1459
1525-1582
  2A:1423-1480
A:1546-1603

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003737901aENSE00002190552X:70586114-70586344231TAF1_HUMAN1-60600--
1.2ENST000003737902ENSE00001693606X:70587349-70587463115TAF1_HUMAN61-99390--
1.3ENST000003737903ENSE00001806491X:70587904-70588020117TAF1_HUMAN99-138400--
1.4ENST000003737904ENSE00001762844X:70595017-70595136120TAF1_HUMAN138-178410--
1.5cENST000003737905cENSE00001746797X:70596863-70597041179TAF1_HUMAN178-237600--
1.6aENST000003737906aENSE00001657433X:70597453-70597671219TAF1_HUMAN238-310730--
1.7ENST000003737907ENSE00001610045X:70598085-70598303219TAF1_HUMAN311-383730--
1.8ENST000003737908ENSE00001671320X:70598674-70598881208TAF1_HUMAN384-453700--
1.9ENST000003737909ENSE00001748084X:70601593-70601769177TAF1_HUMAN453-512600--
1.10ENST0000037379010ENSE00001728655X:70602386-70602513128TAF1_HUMAN512-554430--
1.11ENST0000037379011ENSE00001606772X:70602611-70602718108TAF1_HUMAN555-590360--
1.12ENST0000037379012ENSE00001621948X:70602841-70603014174TAF1_HUMAN591-648580--
1.13ENST0000037379013ENSE00001801775X:70603812-70603985174TAF1_HUMAN649-706580--
1.14ENST0000037379014ENSE00001788701X:70604795-70604899105TAF1_HUMAN707-741350--
1.15bENST0000037379015bENSE00001684911X:70607111-70607311201TAF1_HUMAN742-808670--
1.16bENST0000037379016bENSE00001718382X:70608087-70608228142TAF1_HUMAN809-856480--
1.17bENST0000037379017bENSE00001675273X:70608588-70608718131TAF1_HUMAN856-899440--
1.18bENST0000037379018bENSE00001762617X:70609435-7060951581TAF1_HUMAN900-926270--
1.19ENST0000037379019ENSE00001781380X:70612419-70612568150TAF1_HUMAN927-976500--
1.20ENST0000037379020ENSE00001663592X:70612725-70612844120TAF1_HUMAN977-1016400--
1.21ENST0000037379021ENSE00001765081X:70613151-70613326176TAF1_HUMAN1017-1075590--
1.22aENST0000037379022aENSE00001687499X:70613917-70614095179TAF1_HUMAN1075-1135610--
1.23aENST0000037379023aENSE00001652592X:70617103-70617316214TAF1_HUMAN1135-1206720--
1.24ENST0000037379024ENSE00001801856X:70618422-70618587166TAF1_HUMAN1206-1261560--
1.25ENST0000037379025ENSE00001592652X:70621378-70621589212TAF1_HUMAN1262-1332710--
1.26aENST0000037379026aENSE00002178934X:70626488-70626596109TAF1_HUMAN1332-1368370--
1.27ENST0000037379027ENSE00001710784X:70627424-7062752299TAF1_HUMAN1369-1401331A:1398-142225
1.28ENST0000037379028ENSE00001716532X:70627824-70628001178TAF1_HUMAN1402-1461601A:1423-148260
1.30ENST0000037379030ENSE00001598091X:70641159-7064122668TAF1_HUMAN1461-1483231A:1482-150423
1.31aENST0000037379031aENSE00000978923X:70642967-70643089123TAF1_HUMAN1484-1524411A:1505-154541
1.32aENST0000037379032aENSE00001688409X:70643824-7064391693TAF1_HUMAN1525-1555311A:1546-157631
1.33ENST0000037379033ENSE00001733084X:70644004-7064408885TAF1_HUMAN1556-1584291A:1577-160529
1.35ENST0000037379035ENSE00001619905X:70674020-7067408768TAF1_HUMAN1584-1606231A:1605-162723
1.36ENST0000037379036ENSE00001702834X:70674591-70674707117TAF1_HUMAN1607-1645391A:1628-165225
1.38bENST0000037379038bENSE00001803182X:70678091-70678216126TAF1_HUMAN1646-1687420--
1.40aENST0000037379040aENSE00001787591X:70679402-70679558157TAF1_HUMAN1688-1740530--
1.41aENST0000037379041aENSE00001689245X:70680476-70680653178TAF1_HUMAN1740-1799600--
1.42eENST0000037379042eENSE00001942720X:70683674-706858552182TAF1_HUMAN1799-1872740--

(-) 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:255
 aligned with TAF1_HUMAN | P21675 from UniProtKB/Swiss-Prot  Length:1872

    Alignment length:255
                                  1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626     
          TAF1_HUMAN   1377 RRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAEL 1631
               SCOP domains d3uv5a1 A:1398-1518 automated matches                                                                                    d3uv5a2 A:1519-1652 automated matches                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------I-----------------------------------------------H----------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------BROMODOMAIN_2  PDB: A:1418-1488 UniProt: 1397-1467                     ----------------------------------------------------BROMODOMAIN_2  PDB: A:1541-1611 UniProt: 1520-1590                     ----------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------BROMODOMAIN_1  PDB: A:1423-1480 UniProt: 1402-1459        -----------------------------------------------------------------BROMODOMAIN_1  PDB: A:1546-1603 UniProt: 1525-1582        ------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.27 [INCOMPLETE]   Exon 1.28  PDB: A:1423-1482 UniProt: 1402-1461              ----------------------Exon 1.31a  PDB: A:1505-1545             Exon 1.32a  PDB: A:1546-1576   Exon 1.33  PDB: A:1577-1605  ----------------------Exon 1.36 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.30              ----------------------------------------------------------------------------------------------------Exon 1.35              ------------------------- Transcript 1 (2)
                3uv5 A 1398 RRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAEL 1652
                                  1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627      1637      1647     

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UV5)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TAF1_HUMAN | P21675)
molecular function
    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:0017025    TBP-class protein binding    Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    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:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of 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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, 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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core 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. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:0051123    RNA polymerase II transcriptional preinitiation complex assembly    The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
    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: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:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    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:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    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:0060261    positive regulation of transcription initiation from RNA polymerase II promoter    Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    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:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    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:0005669    transcription factor TFIID complex    A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TAF1_HUMAN | P216751eqf 3aad 3uv4 4rgw 4yym 4yyn 5fur 5i1q 5i29 5mg2

(-) Related Entries Specified in the PDB File

3uv2 3uv4 3uvd 3uvw 3uvx 3uvy 3uw9