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(-) Description

Title :  TFIIIB -TBP/BRF2/DNA AND SANT DOMAIN OF BDP1-
 
Authors :  J. Gouge, A. Vannini, N. Guthertz
Date :  24 Feb 17  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  F,G,H,I,J  (1x)
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gouge, A. Vannini, N. Guthertz
Molecular Mechanisms Of Bdp1 In Tfiiib Assembly And Rna Polymerase Iii Transcription Initiation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR IIIB 50 KDA SUBUNIT
    Chains: A, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BRF2, BRFU, PRO1470
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HTFIIIB50,B-RELATED FACTOR 2,BRF-2,HBRFU
 
Molecule 2 - TATA-BOX-BINDING PROTEIN
    Chains: B, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 159-339
    Gene: TBP, GTF2D1, TF2D, TFIID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TATA SEQUENCE-BINDING PROTEIN,TATA-BINDING FACTOR,TATA-BOX FACTOR,TRANSCRIPTION INITIATION FACTOR TFIID TBP SUBUNIT
 
Molecule 3 - TRANSCRIPTION FACTOR TFIIIB COMPONENT B'' HOMOLOG
    Chains: C, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 241-396
    Gene: BDP1, KIAA1241, KIAA1689, TFNR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSCRIPTION FACTOR IIIB 150,TFIIIB150,TRANSCRIPTION FACTOR-LIKE NUCLEAR REGULATOR
 
Molecule 4 - DNA/RNA (27-MER)
    Chains: D, I
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: BASED ON U6-2 PROMOTER
    Synthetic: YES
 
Molecule 5 - DNA/RNA (25-MER)
    Chains: E, J
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): ABCDE     
Biological Unit 2 (1x):      FGHIJ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY H:326 , PHE H:329 , PRO H:330 , ARG H:332 , HOH H:502binding site for residue NA H 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N9G)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu B:206 -Pro B:207
2Lys B:297 -Pro B:298
3Glu G:206 -Pro G:207
4Lys G:297 -Pro G:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N9G)

(-) Exons   (0, 0)

(no "Exon" information available for 5N9G)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..........hhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhh...........hhhhh.....................hhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n9g A  65 VSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGCCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDLLQHRQSLVRSAFRDGTAEPALLLPPCMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDFQRAQ 406
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   ||  359       369       379       389       399       
                                                                                                                                                                                                                                                                                       318|                                                    
                                                                                                                                                                                                                                                                                        354                                                    


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee.....hhhhhhhhh..eeee...eeeeeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee.....hhhhhhhhh...ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n9g B 157 GPSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKG 334
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        


Chain C from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5n9g C 286 GSTTTYSSFRKNYYSKPWSNKETDMFFLAISMVGTDFSMIGQLFPHRARIEIKNKFKREEKTNGWRIDKAFQEKRPFDFDFFAHLLQKVLAEEEKRK 382
                                   295       305       315       325       335       345       355       365       375       


Chain D from PDB  Type:DNA  Length:27
                                                           
                 5n9g D   2 GGTCACACCTATTTTAAGCCCTTCAAC  28
                                    11        21       


Chain E from PDB  Type:DNA  Length:25
                                                         
                 5n9g E   2 TTGAAGGGCTTAAAATAGGTGTGAC  26
                                    11        21     


Chain F from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..........hhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhh....hhhhh.........hhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n9g F  65 VSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGCCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDLLQHRQSLVRSAFALLLPPCMLKTVTGDENISDSEIEQYLRTPQEVRDFQRAQA 407
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       356       378       388       398         
                                                                                                                                                                                                                                                                                 312|      364|                              
                                                                                                                                                                                                                                                                                  355       377                              


Chain G from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee.....hhhhhhhhh..eeee...eeeeeeee....eeeee....eeeee...hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee.....hhhhhhhhh...eee.......eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n9g G 157 GPSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKG 334
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        


Chain H from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5n9g H 287 STTTYSSFRKNYYSKPWSNKETDMFFLAISMVGTDFSMIGQLFPHRARIEIKNKFKREEKTNGWRIDKAFQEKRPFDFDFFAHLLQKVLAEEEKRKQK 384
                                   296       306       316       326       336       346       356       366       376        


Chain I from PDB  Type:DNA  Length:27
                                                           
                 5n9g I   2 GGTCACACCTATTTTAAGCCCTTCAAC  28
                                    11        21       


Chain J from PDB  Type:DNA  Length:25
                                                         
                 5n9g J   2 TTGAAGGGCTTAAAATAGGTGTGAC  26
                                    11        21
   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 5N9G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N9G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N9G)

(-) Gene Ontology  (40, 51)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRF2_HUMAN | Q9HAW0: 4roc 4rod 4roe
        TBP_HUMAN | P20226: 1c9b 1cdw 1jfi 1nvp 1tgh 4roc 4rod 4roe 5fur 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

(-) Related Entries Specified in the PDB File

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