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(-) Description

Title :  STRUCTURE OF THE NOT-BOX DOMAIN OF HUMAN CNOT3
 
Authors :  A. Boland, Y. Chen, T. Raisch, S. Jonas, E. Izaurralde, O. Weichenriede
Date :  01 Aug 13  (Deposition) - 09 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Gene Regulation, Deadenylation, Mrna Decay, Ccr4-Not, Hydrolase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Boland, Y. Chen, T. Raisch, S. Jonas, D. Kuzuoglu-Ozturk, L. Wohlbold, O. Weichenrieder, E. Izaurralde
Structure And Assembly Of The Not Module Of The Human Ccr4-Not Complex
Nat. Struct. Mol. Biol. V. 20 1289 2013
PubMed-ID: 24121232  |  Reference-DOI: 10.1038/NSMB.2681

(-) Compounds

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM60
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: NOT-BOX DOMAIN, RESIDUES 656-753
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCR4-ASSOCIATED FACTOR 3, LEUKOCYTE RECEPTOR CLUSTER MEMBER 2, CNOT3

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4C0G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C0G)

(-) Exons   (0, 0)

(no "Exon" information available for 4C0G)

(-) 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:90
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:90
                                   668       678       688       698       708       718       728       738       748
          CNOT3_HUMAN   659 TVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE 748
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4c0g A 659 TVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE 748
                                   668       678       688       698    || 708       718       728       738       748
                                                                      703-MSE                                         
                                                                       704-MSE                                        


Chain B from PDB  Type:PROTEIN  Length:97
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:97
                                   664       674       684       694       704       714       724       734       744       
          CNOT3_HUMAN   655 PHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDRD 751
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4c0g B 655 AHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDRD 751
                                   664       674       684       694       704       714       724       734       744       
                                                                          703-MSE                                            
                                                                           704-MSE                                           


Chain C from PDB  Type:PROTEIN  Length:96
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:96
                                   664       674       684       694       704       714       724       734       744      
          CNOT3_HUMAN   655 PHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4c0g C 655 AHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
                                   664       674       684       694       704       714       724       734       744      
                                                                          703-MSE                                           
                                                                           704-MSE                                          


Chain D from PDB  Type:PROTEIN  Length:96
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:96
                                   664       674       684       694       704       714       724       734       744      
          CNOT3_HUMAN   655 PHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4c0g D 655 AHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
                                   664       674       684       694       704       714       724       734       744      
                                                                          703-MSE                                           
                                                                           704-MSE                                          


Chain E from PDB  Type:PROTEIN  Length:91
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:91
                                   667       677       687       697       707       717       727       737       747 
          CNOT3_HUMAN   658 DTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE 748
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4c0g E 658 DTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE 748
                                   667       677       687       697     ||707       717       727       737       747 
                                                                       703-MSE                                         
                                                                        704-MSE                                        


Chain F from PDB  Type:PROTEIN  Length:93
 aligned with CNOT3_HUMAN | O75175 from UniProtKB/Swiss-Prot  Length:753

    Alignment length:93
                                   667       677       687       697       707       717       727       737       747   
          CNOT3_HUMAN   658 DTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh...eee....eeeee....eee...eeeeeeeeee....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4c0g F 658 DTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYmmWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLEDR 750
                                   667       677       687       697     ||707       717       727       737       747   
                                                                       703-MSE                                           
                                                                        704-MSE
   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 4C0G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C0G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C0G)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (CNOT3_HUMAN | O75175)
molecular function
    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).
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:2000036    regulation of stem cell population maintenance    Any process that modulates the frequency, rate or extent of stem cell population maintenance.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates 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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001829    trophectodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        CNOT3_HUMAN | O75175: 4c0d 5fu6 5fu7

(-) Related Entries Specified in the PDB File

4c0d STRUCTURE OF THE NOT MODULE OF THE HUMAN CCR4-NOT COMPLEX (CNOT1-CNOT2-CNOT3)
4c0f STRUCTURE OF THE NOT-BOX DOMAIN OF HUMAN CNOT2