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(-) Description

Title :  NOT MODULE OF THE HUMAN CCR4-NOT COMPLEX (CRYSTALLIZATION MUTANT)
 
Authors :  T. Raisch, D. Bhandari, K. Sabath, S. Helms, E. Valkov, O. Weichenriede E. Izaurralde
Date :  21 Jan 16  (Deposition) - 23 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Gene Regulation, Deadenylation, Mrna Decay, Ccr4-Not, Transcription, Translational Repression (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Raisch, D. Bhandari, K. Sabath, S. Helms, E. Valkov, O. Weichenrieder, E. Izaurralde
Distinct Modes Of Recruitment Of The Ccr4-Not Complex By Drosophila And Vertebrate Nanos
Embo J. V. 35 974 2016
PubMed-ID: 26968986  |  Reference-DOI: 10.15252/EMBJ.201593634

(-) Compounds

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCN(PNYC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1833-2361
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCR4-ASSOCIATED FACTOR 1, NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG, NOT1H, HNOT1, CNOT1
 
Molecule 2 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCN(PNEA)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 350-540
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCR4-ASSOCIATED FACTOR 2, CNOT2
 
Molecule 3 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCN(PNEA)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 607-748
    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):    DEF
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FU6)

(-) Sites  (0, 0)

(no "Site" information available for 5FU6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FU6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:2188 -Pro A:2189
2Arg A:2316 -Pro A:2317
3Ser D:2188 -Pro D:2189
4Arg D:2316 -Pro D:2317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FU6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FU6)

(-) Exons   (0, 0)

(no "Exon" information available for 5FU6)

(-) 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:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhh.....hhhhhhhhh.......................................hhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fu6 A 1842 YDDPPGLREKAEYLLREWVNLYHSAAAGRDSTKAFSAFVGQMHQQGILKTDDLITRFFRLCTEMCVEISYRAQAEQQHNPAANPTMIRAKCYHNLDAFVRLIALLVKHSGEATNTVTKINLLNKVLGIVVGVLLQDHDVRQSEFQQLPYHRIFIMLLLELNAPTINFQTLTAFCNTFHILRPTKAPGFVYAWLELISHRIFIARMLAHTPQQKGWPMYAQLLIDLFKYLAPFLRNVELTKPMQILYKGTLRVLLVLLHDFPEFLCDYHYGFCDVIPPNCIQLRNLILSAFPRNMRLPDPFTPNLKVDMLSEINIAPRILTNFTGVMPPQFKKDLDSYLKTRSPVTFLSDLRSNLQVSNEPGNRYNLQLINALVLYVGTQAIAHIHNKGSTPSMSTITHSAHMDIFQNLAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCTMLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPAFKFWNHEFVEEEPEIEKLFQSVAQCCM 2361
                                  1851      1861      1871      1881      1891      1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001  ||  2016      2026      2036      2046      2056      2066      2076      2086      2096      2106      2116      2126      2136      2146      2156      2166      2176      2186      2196      2206      2216      2226      2236      2246      2256      2266      2276      2286      2296      2306      2316      2326      2336      2346      2356     
                                                                                                                                                                                           2004|                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                            2010                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.......................................................................hhhhhhhhhh....hhhhhhhhhhhh..eeee....eeee........eee..eeeeeeeeee....eeeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fu6 B  349 EMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWASSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYMNGGDVLQLLAAVELFNRDWRYHKEERVWITRAPGMEPTMKTNTYERGTYYFFDCLNWRKVAKEFHLEYDKLEERPHLPSTFNYNPAQQAF  540
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538  


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....................................hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh..eeee....eeeee.....eee..eeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fu6 C  601 GPHMLELTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE  748
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740        


Chain D from PDB  Type:PROTEIN  Length:516
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhh.....hhhhhhhhh.......................................hhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fu6 D 1842 YDDPPGLREKAEYLLREWVNLYHSAAAGRDSTKAFSAFVGQMHQQGILKTDDLITRFFRLCTEMCVEISYRAQAEQQHNPAANPTMIRAKCYHNLDAFVRLIALLVKHSGEATNTVTKINLLNKVLGIVVGVLLQDHDVRQSEFQQLPYHRIFIMLLLELNALETINFQTLTAFCNTFHILRPTKAPGFVYAWLELISHRIFIARMLAHTPQQKGWPMYAQLLIDLFKYLAPFLRNVELTKPMQILYKGTLRVLLVLLHDFPEFLCDYHYGFCDVIPPNCIQLRNLILSAFPRNMRLPDPFTPNLKVDMLSEINIAPRILTNFTGVMPPQFKKDLDSYLKTRSPVTFLSDLRSNLQVSNEPGNRYNLQLINALVLYVGTQAIAHIHNKGSTPSMSTITHSAHMDIFQNLAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCTMLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPAFKFWNHEFVEEEPEIEKLFQSVAQCCM 2361
                                  1851      1861      1871      1881      1891      1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001 ||   2015      2025      2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175      2185      2195      2205      2215      2225      2235      2245      2255      2265      2275      2285      2295      2305      2315      2325      2335      2345      2355      
                                                                                                                                                                                          2003|                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                           2008                                                                                                                                                                                                                                                                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh.......................................................................hhhhhhhhhh....hhhhhhhhhhhh..eeee....eeee........eee..eeeeeeeeee....eeeeeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fu6 E  350 MVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWASSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYMNGGDVLQLLAAVELFNRDWRYHKEERVWITRAPGMEPTMKTNTYERGTYYFFDCLNWRKVAKEFHLEYDKLEERPHLPSTFNYNPAQQAF  540
                                   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539 


Chain F from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....................................hhhhhh..hhhhhhhhhh....hhhhhhhhhhhh..eeee....eeeee.....eee..eeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fu6 F  601 GPHMLELTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE  748
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740
   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 5FU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FU6)

(-) Gene Ontology  (40, 80)

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  Cis Peptide Bonds
    Arg A:2316 - Pro A:2317   [ RasMol ]  
    Arg D:2316 - Pro D:2317   [ RasMol ]  
    Ser A:2188 - Pro A:2189   [ RasMol ]  
    Ser D:2188 - Pro D:2189   [ RasMol ]  
 
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  5fu6
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  CNOT1_HUMAN | A5YKK6
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  CNOT2_HUMAN | Q9NZN8
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  CNOT3_HUMAN | O75175
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 Related Entries

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

UniProtKB/Swiss-Prot
        CNOT1_HUMAN | A5YKK6: 4c0d 4cqo 4cru 4crv 4crw 4ct4 4ct6 4ct7 4gmj 4gml 4j8s 5anr 5fu7
        CNOT2_HUMAN | Q9NZN8: 4c0d 4c0f 5fu7
        CNOT3_HUMAN | O75175: 4c0d 4c0g 5fu7

(-) Related Entries Specified in the PDB File

5fu7 DROSOPHILA NANOS NBR PEPTIDE BOUND TO THE NOT MODULE OF THE HUMAN CCR4-NOT COMPLEX