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(-) Description

Title :  STRUCTURAL DETAILS OF UFD1 BINDING TO P97
 
Authors :  L. T. M. Le, J. K. Yang
Date :  26 May 16  (Deposition) - 04 Jan 17  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ufd1, Shp Box, P97, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. T. M. Le, W. Kang, J. Y. Kim, O. T. T. Le, S. Y. Lee, J. K. Yang
Structural Details Of Ufd1 Binding To P97 And Their Functional Implications In Er-Associated Degradation
Plos One V. 11 63394 2016
PubMed-ID: 27684549  |  Reference-DOI: 10.1371/JOURNAL.PONE.0163394

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    ChainsA
    EC Number3.6.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 21-191
    GeneVCP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING PROTEIN,VCP
 
Molecule 2 - PEPTIDE FROM UBIQUITIN FUSION DEGRADATION PROTEIN 1 HOMOLOG
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneUFD1L
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5B6C)

(-) Sites  (0, 0)

(no "Site" information available for 5B6C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B6C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:169 -Pro A:170
2Ser A:171 -Pro A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B6C)

(-) Exons   (0, 0)

(no "Exon" information available for 5B6C)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee........eeeehhhhhhhh......eeeee.....eeeeeeee.......eee.hhhhhhhhh.....eeeeee........eeeeeehhhhhh....hhhhhhhhhhhh...eeee...eeee......eeeeeeeee...eeee....eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b6c A  19 GSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRA 192
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    

Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5b6c B 225 FRAFSGSGNRL 235
                                   234 

   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 5B6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B6C)

(-) Gene Ontology  (76, 91)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:169 - Pro A:170   [ RasMol ]  
    Ser A:171 - Pro A:172   [ RasMol ]  
 

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  UFD1_HUMAN | Q92890
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 Related Entries

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

UniProtKB/Swiss-Prot
        TERA_HUMAN | P550723ebb 3hu1 3hu2 3hu3 3qc8 3qq7 3qq8 3qwz 3tiw 4kdi 4kdl 4kln 4ko8 4kod 4p0a 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifs 5ifw 5x4l
        UFD1_HUMAN | Q928902yuj 5c1b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5B6C)