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(-) Description

Title :  DROSOPHILA NANOS NBR PEPTIDE BOUND TO THE NOT MODULE OF THE HUMAN CCR4-NOT COMPLEX
 
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 :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (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, E
    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
 
Molecule 2 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
    Chains: B, 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 350-540
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCR4-ASSOCIATED FACTOR 2
 
Molecule 3 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
    Chains: C, G
    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
 
Molecule 4 - NANOS, ISOFORM B
    Chains: D, H
    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 MODULE BINDING REGION (NBR), RESIDUES 116-163
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FU7)

(-) Sites  (0, 0)

(no "Site" information available for 5FU7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FU7)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FU7)

(-) Exons   (0, 0)

(no "Exon" information available for 5FU7)

(-) 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:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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
                5fu7 A 1839 ASEYDDPPGLREKAEYLLREWVNLYHSAAAGRDSTKAFSAFVGQMHQQGILKTDDLITRFFRLCTEMCVEISYRAQAEQQHNPAANPTMIRAKCYHNLDAFVRLIALLVKHSGEATNTVTKINLLNKVLGIVVGVLLQDHDVRQSEFQQLPYHRIFIMLLLELNALETINFQTLTAFCNTFHILRPTKAPGFVYAWLELISHRIFIARMLAHTPQQKGWPMYAQLLIDLFKYLAPFLRNVELTKPMQILYKGTLRVLLVLLHDFPEFLCDYHYGFCDVIPPNCIQLRNLILSAFPRNMRLPDPFTPNLKVDMLSEINIAPRILTNFTGVMPPQFKKDLDSYLKTRSPVTFLSDLRSNLQVSNEPGNRYNLQLINALVLYVGTQAIAHIHNKGSTPSMSTITHSAHMDIFQNLAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCTMLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPAFKFWNHEFVEEEPEIEKLFQSVAQCCM 2361
                                  1848      1858      1868      1878      1888      1898      1908      1918      1928      1938      1948      1958      1968      1978      1988      1998    ||2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182      2192      2202      2212      2222      2232      2242      2252      2262      2272      2282      2292      2302      2312      2322      2332      2342      2352         
                                                                                                                                                                                             2003|                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                              2008                                                                                                                                                                                                                                                                                                                                                                 


Chain B 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
                5fu7 B  349 EMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWASSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYMNGGDVLQLLAAVELFNRDWRYHKEERVWITRAPGMEPTMKTNTYERGTYYFFDCLNWRKVAKEFHLEYDKLEERPHLPSTFNYNPAQQA  539
                                   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
                5fu7 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:33
                                                                  
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                5fu7 D  120 TDEIARSLKIFAQVTSMQDVMQEFATNGYASDD  161
                                   129    || 148       158   
                                        134|                 
                                         144                 


Chain E from PDB  Type:PROTEIN  Length:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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
                5fu7 E 1841 EYDDPPGLREKAEYLLREWVNLYHSAAAGRDSTKAFSAFVGQMHQQGILKTDDLITRFFRLCTEMCVEISYRAQAEQQHNPAANPTMIRAKCYHNLDAFVRLIALLVKHSGEATNTVTKINLLNKVLGIVVGVLLQDHDVRQSEFQQLPYHRIFIMLLLELNAINFQTLTAFCNTFHILRPTKAPGFVYAWLELISHRIFIARMLAHTPQQKGWPMYAQLLIDLFKYLAPFLRNVELTKPMQILYKGTLRVLLVLLHDFPEFLCDYHYGFCDVIPPNCIQLRNLILSAFPRNMRLPDPFTPNLKVDMLSEINIAPRILTNFTGVMPPQFKKDLDSYLKTRSPVTFLSDLRSNLQVSNEPGNRYNLQLINALVLYVGTQAIAHIHNKGSTPSMSTITHSAHMDIFQNLAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCTMLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPAFKFWNHEFVEEEPEIEKLFQSVAQCCM 2361
                                  1850      1860      1870      1880      1890      1900      1910      1920      1930      1940      1950      1960      1970      1980      1990      2000  ||  2017      2027      2037      2047      2057      2067      2077      2087      2097      2107      2117      2127      2137      2147      2157      2167      2177      2187      2197      2207      2217      2227      2237      2247      2257      2267      2277      2287      2297      2307      2317      2327      2337      2347      2357    
                                                                                                                                                                                           2003|                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                            2011                                                                                                                                                                                                                                                                                                                                                              


Chain F 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
                5fu7 F  349 EMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWASSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYMNGGDVLQLLAAVELFNRDWRYHKEERVWITRAPGMEPTMKTNTYERGTYYFFDCLNWRKVAKEFHLEYDKLEERPHLPSTFNYNPAQQA  539
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 


Chain G 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
                5fu7 G  601 GPHMLELTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE  748
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740        


Chain H from PDB  Type:PROTEIN  Length:30
                                                               
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh..hhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                5fu7 H  120 TDEIARSLKIFAGSMQDVMQEFATNGYASD  160
                                   129 ||    150       160
                                     131|                 
                                      143
   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 5FU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FU7)

(-) Gene Ontology  (40, 80)

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  Cis Peptide Bonds
    Arg A:2316 - Pro A:2317   [ RasMol ]  
    Arg E:2316 - Pro E:2317   [ RasMol ]  
    Ser A:2188 - Pro A:2189   [ RasMol ]  
    Ser E:2188 - Pro E:2189   [ RasMol ]  
 
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  5fu7
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  A0A0B4KGY5_D | A0A0B4KGY5
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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 5fu6
        CNOT2_HUMAN | Q9NZN8: 4c0d 4c0f 5fu6
        CNOT3_HUMAN | O75175: 4c0d 4c0g 5fu6

(-) Related Entries Specified in the PDB File

5fu6 NOT MODULE OF THE HUMAN CCR4-NOT COMPLEX (CRYSTALLIZATION MUTANT).