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(-) Description

Title :  CRYSTAL STRUCTURE OF ENCEPHALITOZOON CUNICULI TAF5 N-TERMINAL DOMAIN
 
Authors :  C. Romier, N. James, C. Birck, J. Cavarelli, C. Vivares, M. A. Collart,
Date :  28 Aug 06  (Deposition) - 10 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Taf5, Tfiid, Wd Repeat, Initiation, Transcription, Initiation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Romier, N. James, C. Birck, J. Cavarelli, C. Vivares, M. A. Collart, D. Moras
Crystal Structure, Biochemical And Genetic Characterization Of Yeast And E. Cuniculi Taf(Ii)5 N-Terminal Domain: Implications For Tfiid Assembly.
J. Mol. Biol. V. 368 1292 2007
PubMed-ID: 17397863  |  Reference-DOI: 10.1016/J.JMB.2007.02.039

(-) Compounds

Molecule 1 - TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 72/90-100 KDA
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: N-TERMINAL DOMAIN, RESIDUES 16-149
    Organism Scientific: ENCEPHALITOZOON CUNICULI
    Organism Taxid: 6035
    Synonym: TAF5

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2J4B)

(-) Sites  (0, 0)

(no "Site" information available for 2J4B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J4B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J4B)

(-) Exons   (0, 0)

(no "Exon" information available for 2J4B)

(-) 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:129
 aligned with TAF5_ENCCU | Q8SQS4 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:131
                                    27        37        47        57        67        77        87        97       107       117       127       137       147 
           TAF5_ENCCU    18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
               SCOP domains d2j4ba1 A:18-148 TAF5 subunit of TFIID                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh--hhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4b A  18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDH--KSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
                                    27        37        47        57        67        |- |      87        97       107       117       127       137       147 
                                                                                     76 79                                                                     


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with TAF5_ENCCU | Q8SQS4 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:133
                                    26        36        46        56        66        76        86        96       106       116       126       136       146   
           TAF5_ENCCU    17 DQMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVGP 149
               SCOP domains d2j4bb_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4b B  17 DQMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVGP 149
                                    26        36        46        56        66        76        86        96       106       116       126       136       146   


Chain C from PDB  Type:PROTEIN  Length:133
 aligned with TAF5_ENCCU | Q8SQS4 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:133
                                    25        35        45        55        65        75        85        95       105       115       125       135       145   
           TAF5_ENCCU    16 KDQMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
               SCOP domains d2j4bc_ C: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4b C  16 KDQMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
                                    25        35        45        55        65        75        85        95       105       115       125       135       145   


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with TAF5_ENCCU | Q8SQS4 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:131
                                    27        37        47        57        67        77        87        97       107       117       127       137       147 
           TAF5_ENCCU    18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
               SCOP domains d2j4bd_ D: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4b D  18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYVG 148
                                    27        37        47        57        67        77        87        97       107       117       127       137       147 


Chain E from PDB  Type:PROTEIN  Length:130
 aligned with TAF5_ENCCU | Q8SQS4 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:130
                                    27        37        47        57        67        77        87        97       107       117       127       137       147
           TAF5_ENCCU    18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYV 147
               SCOP domains d2j4be_ E: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhh.hhhhhhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4b E  18 QMETSYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRGDHYNKSEEIKQFESIYTVQHIHENNFAYTFKNSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHLDIKVYV 147
                                    27        37        47        57        67        77        87        97       107       117       127       137       147
   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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J4B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J4B)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (TAF5_ENCCU | Q8SQS4)
molecular function
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.
cellular component
    GO:0000124    SAGA complex    A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8.
    GO:0046695    SLIK (SAGA-like) complex    A SAGA-type histone acetyltransferase complex that contains Rtg2 and a smaller form of Spt7 than the fungal SAGA complex, and lacks Spt8. The complex is involved in the yeast retrograde response pathway, which is important for gene expression changes during mitochondrial dysfunction.
    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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2j49 CRYSTAL STRUCTURE OF YEAST TAF5 N-TERMINAL DOMAIN