Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A HUMAN 4E-T - DDX6 - CNOT1 COMPLEX
 
Authors :  J. Basquin, S. Oezguer, E. Conti
Date :  08 Sep 15  (Deposition) - 21 Oct 15  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A (1x),B (1x),C (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x)
Keywords :  Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ozgur, J. Basquin, A. Kamenska, W. Filipowicz, N. Standart, E. Cont
Structure Of A Human 4E-T/Ddx6/Cnot1 Complex Reveals The Different Interplay Of Ddx6-Binding Proteins With The Ccr4- Not Complex.
Cell Rep. V. 13 703 2015
PubMed-ID: 26489469  |  Reference-DOI: 10.1016/J.CELREP.2015.09.033

(-) Compounds

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC_HIS_SUMO
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Fragment: MIF4G DOMAIN, UNP RESIDUES 1063-1314
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CCR4-ASSOCIATED FACTOR 1, NOT1H, NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG, HNOT1, CNOT1-MIF4G DOMAIN
 
Molecule 2 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
    Chains: B
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC_HIS_SUMO
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Fragment: RECA1 AND RECA2, UNP RESIDUES 95-469
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ATP-DEPENDENT RNA HELICASE P54, DEAD BOX PROTEIN 6, ONCOGENE RCK, DDX6
 
Molecule 3 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC_HIS_SUMO
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 199-239
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 4E-T, EIF4E TRANSPORTER, EUKARYOTIC TRANSLATION INITIATION FACTOR 4E NUCLEAR IMPORT FACTOR 1,4ET

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A (1x)B (1x)C (1x)
Biological Unit 2 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5ANR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:1249 -Pro A:1250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ANR)

(-) 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:245
                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh........hhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhh.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5anr A 1065 INTTNIDTLLVATDQTERIVEPPENIQEKIAFIFNNLSQSNMTQKVEELKETVKEEFMPWVSQYLVMKRVSIEPNFHSLYSNFLDTLKNPEFNKMVLNETYRNIKVLLTSDKAAANFSDRSLLKNLGHWLGMITLAKNKPILHTDLDVKSLLLEAYVKGQQELLYVVPFVAKVLESSIRSVVFRPPNPWTMAIMNVLAELHQEHDLKLNLKFEIEVLCKNLALDINELKPGNLLKDKDRLKNLDE 1309
                                  1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304     


Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh.....eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeee..........eeeeee.hhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeee........eeeeee.....hhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5anr B   95 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFDIQAVNVVINFDFPKLAETYLHRIGRSGLGLAINLITYDDRFNLKSIEEQLGTEIKPIPS  462
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394|      408       418       432       442       452       462
                                                                                                                                                                                                                                                                                                                                     394|                        426|                               
                                                                                                                                                                                                                                                                                                                                      399                         431                               


Chain C from PDB  Type:PROTEIN  Length:23
                                                        
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ...hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                5anr C  216 EEEPEWFSAGPTSQSETIELTGF  238
                                   225       235
   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 5ANR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (57, 75)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5anr)
 
  Sites
(no "Sites" information available for 5anr)
 
  Cis Peptide Bonds
    Pro A:1249 - Pro A:1250   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5anr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  4ET_HUMAN | Q9NRA8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CNOT1_HUMAN | A5YKK6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DDX6_HUMAN | P26196
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.4.13
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  4ET_HUMAN | Q9NRA8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CNOT1_HUMAN | A5YKK6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DDX6_HUMAN | P26196
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5fu6 5fu7
        DDX6_HUMAN | P26196: 1vec 2wax 2way 4crw 4ct4 4ct5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5ANR)