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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL SPT4/5 BOUND TO THE RNAP CLAMP DOMAIN
 
Authors :  F. W. Martinez-Rucobo
Date :  15 Feb 11  (Deposition) - 23 Mar 11  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Transcription, Fusion Protein, Chimera Protein, Multiprotein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. W. Martinez-Rucobo, S. Sainsbury, A. C. Cheung, P. Cramer
Architecture Of The Rna Polymerase-Spt4/5 Complex And Basis Of Universal Transcription Processivity.
Embo J. V. 30 1302 2011
PubMed-ID: 21386817  |  Reference-DOI: 10.1038/EMBOJ.2011.64

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT B, DNA-DIRECTED RNA POLYMERASE SUBUNIT A', DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DNA-DIRECTED RNA POLYMERASE SUBUNIT B (RESIDUES 1053-1115), DNA-DIRECTED RNA POLYMERASE SUBUNIT A' (RESIDUES 3-318), DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' (RESIDUES 334-371)
    Gene: PF1563
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
 
Molecule 2 - TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PF1990
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
 
Molecule 3 - DNA-DIRECTED RNA POLYMERASE, SUBUNIT E''
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PF0255
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ADE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:161 , CYS A:164 , CYS A:208 , PRO A:209BINDING SITE FOR RESIDUE ZN A 2000
2AC2SOFTWARECYS A:121 , CYS A:124 , CYS A:131 , HIS A:134BINDING SITE FOR RESIDUE ZN A 2001
3AC3SOFTWARECYS A:8 , CYS A:11 , CYS A:26 , CYS A:29BINDING SITE FOR RESIDUE ZN A 2002
4AC4SOFTWARECYS E:6 , CYS E:9 , CYS E:18 , CYS E:21BINDING SITE FOR RESIDUE ZN E 100

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QQC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QQC)

(-) Exons   (0, 0)

(no "Exon" information available for 3QQC)

(-) 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:381
 aligned with Q8U0M4_PYRFU | Q8U0M4 from UniProtKB/TrEMBL  Length:907

    Alignment length:432
                                                                                   2                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                  1|       3                                                                                                                                                                                                                                                                                                                                                                                
                                     -         -         -         -         -    ||   -   |     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369  
         Q8U0M4_PYRFU     - ------------------------------------------------------MK-------KVIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVCPHCGAPQYPIKFEKPTIYWEIRKDEQGNEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPMISINEVGVPVEVAMELTVPEKVTEFNIERLRKMVLNG 371
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------RNA_pol_Rpb1_1-3qqcA01 A:67-371                                                                                                                                                                                                                                                                                                                    ------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......eee....eee.........eeeeeehhhhhhhhhhhhhh....eeeee..eeeeee....hhhhhhhheeee........----.................................eeeeeeeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....-------.........eeee...---...eeeehhhhhhhhhhhh...hhhhh.......hhhh.eeeeeee.hhhhh.....---....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..................hhhhhhh.----------------------------------...hhhhhhhhhhhh.eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qqc A   2 KTEVWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSEKVIGSIEFGILSPQEIRKMSAVEVTVPDTYD----PIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERMVCP-------PIKFEKPTIYWEIRKD---NEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITL---IRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKG----------------------------------FEITVQHLFEAAEKGEVDNLNGVIENVLIG 436
                                    11        21        31        41        51        61  ||    73        83        93   |   103       113       123       133       143       153       163       173       183       193       203     |   -   |   223        |-  |    243       253       263       273       283        |-  |    303       313       323       333       343       353       363       | -         -         -         -  |    414       424       434  
                                                                                         64|                            97  102                                                                                                        209     217            232 236                                                     292 296                                                                        371                                407                             
                                                                                          67                                                                                                                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:82
 aligned with SPT5_PYRFU | Q8TZK1 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:82
                                    13        23        33        43        53        63        73        83  
           SPT5_PYRFU     4 KIFAVRVTHGQEETTAKLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEE  85
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh.........eeee......eeeee..hhhhhhhhhh.............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3qqc D   4 KIFAVRVTHGQEETTAKLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEE  85
                                    13        23        33        43        53        63        73        83  


Chain E from PDB  Type:PROTEIN  Length:58
 aligned with SPT4_PYRFU | Q8U440 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:58
                                    12        22        32        42        52        
           SPT4_PYRFU     3 EKACRHCHYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSEIAKKIGAKVPGKYAIRV  60
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....ee............ee.....eeee.....hhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 3qqc E   3 EKACRHCHYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSEIAKKIGAKVPGKYAIRV  60
                                    12        22        32        42        52
   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 3QQC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RNA_pol_Rpb1_1] (37)

(-) Gene Ontology  (15, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8U0M4_PYRFU | Q8U0M4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain D   (SPT5_PYRFU | Q8TZK1)
molecular function
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
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:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain E   (SPT4_PYRFU | Q8U440)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.

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  RPOA2_PYRFU | Q8U0M5
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  SPT5_PYRFU | Q8TZK1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPT4_PYRFU | Q8U440: 1ryq 3p8b
        SPT5_PYRFU | Q8TZK1: 3p8b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QQC)