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(-) Description

Title :  N-TERMINAL DOMAIN OF THE YEAST NOT1
 
Authors :  J. Basquin, E. Conti
Date :  26 Aug 12  (Deposition) - 21 Nov 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Basquin, V. V. Roudko, M. Rode, C. Basquin, B. Seraphin, E. Conti
Architecture Of The Nuclease Module Of The Yeast Ccr4-Not Complex: The Not1-Caf1-Ccr4 Interaction.
Mol. Cell V. 48 207 2012
PubMed-ID: 22959269  |  Reference-DOI: 10.1016/J.MOLCEL.2012.08.014

(-) Compounds

Molecule 1 - GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYS STAR
    Expression System Vector: PEC_SUMO_HT_A
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 151-753
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE S288C
    Organism Taxid: 559292
    Synonym: CELL DIVISION CYCLE PROTEIN 39, NOT1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 29)

Asymmetric/Biological Unit (1, 29)
No.NameCountTypeFull Name
1AU29Ligand/IonGOLD ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:424 , SER A:461BINDING SITE FOR RESIDUE AU A1747
02AC2SOFTWARESER A:504 , PRO A:505 , CYS A:549 , PRO A:550BINDING SITE FOR RESIDUE AU A1748
03AC3SOFTWARECYS A:486 , ILE A:490 , LEU A:531BINDING SITE FOR RESIDUE AU A1749
04AC4SOFTWAREASN A:238 , VAL A:239BINDING SITE FOR RESIDUE AU A1750
05AC5SOFTWAREMET A:601 , CYS A:639BINDING SITE FOR RESIDUE AU A1751
06AC6SOFTWARELEU A:412 , LYS A:439BINDING SITE FOR RESIDUE AU A1752
07AC7SOFTWAREGLN A:705BINDING SITE FOR RESIDUE AU A1753
08AC8SOFTWAREPHE A:357BINDING SITE FOR RESIDUE AU A1755
09AC9SOFTWAREALA A:569BINDING SITE FOR RESIDUE AU A1756
10BC1SOFTWARECYS A:320BINDING SITE FOR RESIDUE AU A1757
11BC2SOFTWAREALA A:233BINDING SITE FOR RESIDUE AU A1802
12BC3SOFTWAREPRO B:424BINDING SITE FOR RESIDUE AU B1747
13BC4SOFTWAREPHE B:357BINDING SITE FOR RESIDUE AU B1748
14BC5SOFTWAREALA B:456 , CYS B:486 , ILE B:490 , LEU B:531BINDING SITE FOR RESIDUE AU B1749
15BC6SOFTWARESER B:279BINDING SITE FOR RESIDUE AU B1750
16BC7SOFTWAREHIS B:642 , ALA B:643BINDING SITE FOR RESIDUE AU B1751
17BC8SOFTWARELYS B:616 , GLU B:620BINDING SITE FOR RESIDUE AU B1752
18BC9SOFTWAREASN B:318 , CYS B:320BINDING SITE FOR RESIDUE AU B1753
19CC1SOFTWAREPRO B:505 , ASP B:509BINDING SITE FOR RESIDUE AU B1754
20CC2SOFTWAREARG B:689BINDING SITE FOR RESIDUE AU B1755
21CC3SOFTWAREMET B:395 , LYS B:439BINDING SITE FOR RESIDUE AU B1756
22CC4SOFTWARELYS B:500BINDING SITE FOR RESIDUE AU B1801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B8B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:453 -Pro A:454
2Ala B:453 -Pro B:454

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B8B)

(-) Exons   (0, 0)

(no "Exon" information available for 4B8B)

(-) 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:528
 aligned with NOT1_YEAST | P25655 from UniProtKB/Swiss-Prot  Length:2108

    Alignment length:555
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741     
           NOT1_YEAST   192 LEGESLNDLLALLLSEILSPGSQNLQNDPTRSWLTPPMVLDATNRGNVIARSISSLQANQINWNRVFNLMSTKYFLSAPLMPTTASLSCLFAALHDGPVIDEFFSCDWKVIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIASLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVLLIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINSDDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLKTKVSPSNVDVVLESLEVQTKMTDTNTPFRSLKTFDLFAFHSLIEVLNKCPLDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKEMQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTFFQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMFKFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAAT 746
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhh..----------------------hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...---...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhh...............hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhh..--.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b8b A 192 LEGESLNDLLALLLSEILS----------------------ATNRGNVIARSISSLQANQINWNRVFNLMSTKYFL---LMPTTASLSCLFAALHDGPVIDEFFSCDWKVIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIASLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVLLIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINSDDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLKTKVSPSNVDVVLESLEVQTKMTD--TPFRSLKTFDLFAFHSLIEVLNKCPLDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKEMQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTFFQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMFKFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAAT 746
                                   201        |-         -         - |     241       251       261     | 271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521 |  |  531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741     
                                            210                    233                               267 271                                                                                                                                                                                                                                                         523  |                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                        526                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:529
 aligned with NOT1_YEAST | P25655 from UniProtKB/Swiss-Prot  Length:2108

    Alignment length:555
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741     
           NOT1_YEAST   192 LEGESLNDLLALLLSEILSPGSQNLQNDPTRSWLTPPMVLDATNRGNVIARSISSLQANQINWNRVFNLMSTKYFLSAPLMPTTASLSCLFAALHDGPVIDEFFSCDWKVIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIASLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVLLIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINSDDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLKTKVSPSNVDVVLESLEVQTKMTDTNTPFRSLKTFDLFAFHSLIEVLNKCPLDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKEMQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTFFQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMFKFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAAT 746
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...----------------------.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...----..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhh......................hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b8b B 192 LEGESLNDLLALLLSEILS----------------------ATNRGNVIARSISSLQANQINWNRVFNLMSTKYFL----MPTTASLSCLFAALHDGPVIDEFFSCDWKVIFKLDLAIQLHKWSVQNGCFDLLNAEGTRKVSETIPNTKQSLLYLLSIASLNLELFLQREELSDGPMLAYFQECFFEDFNYAPEYLILALVKEMKRFVLLIENRTVIDEILITLLIQVHNKSPSSFKDVISTITDDSKIVDAAKIIINSDDAPIANFLKSLLDTGRLDTVINKLPFNEAFKILPCARQIGWEGFDTFLKTKVSPSNVDVVLESLEVQTKMTDTNTPFRSLKTFDLFAFHSLIEVLNKCPLDVLQLQRFESLEFSLLIAFPRLINFGFGHDEAILANGDIAGINNDIEKEMQNYLQKMYSGELAIKDVIELLRRLRDSDLPRDQEVFTCITHAVIAESTFFQDYPLDALATTSVLFGSMILFQLLRGFVLDVAFRIIMRFAKEPPESKMFKFAVQAIYAFRIRLAEYPQYCKDLLRDVPALKSQAQVYQSIVEAAT 746
                                   201        |-         -         - |     241       251       261     |   -|      281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741     
                                            210                    233                               267  272
   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 4B8B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B8B)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NOT1_YEAST | P25655)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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: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.
biological process
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0007124    pseudohyphal growth    A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000749    response to pheromone involved in conjugation with cellular fusion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus that contributes to the process of conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0030015    CCR4-NOT core complex    The core of the CCR4-NOT complex. In Saccharomyces the CCR4-NOT core complex comprises Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p.
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NOT1_YEAST | P25655: 4b89 4b8a 4b8c 4cv5

(-) Related Entries Specified in the PDB File

4b89 MIF4G DOMAIN OF THE YEAST NOT1
4b8a STRUCTURE OF YEAST NOT1 MIF4G DOMAIN CO-CRYSTALLIZED WITH CAF1
4b8c NUCLEASE MODULE OF THE YEAST CCR4-NOT COMPLEX