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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE INTERACTION OF P97 N-TERMINUS DOMAIN AND VBM MOTIF IN RHOMBOID PROTEASE, RHBDL4
 
Authors :  J. J. Lim, Y. Lee, T. T. Ly, J. Y. Kang, J. -G. Lee, J. Y. An, H. -S. Youn, K. R. T. G. Kim, J. K. Yang, Y. Jun, S. H. Eom
Date :  12 Nov 15  (Deposition) - 14 Sep 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Barrel, Atpase, Rhbdl4 Vbm Motif, Ubiquitin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. J. Lim, Y. Lee, T. T. Ly, J. Y. Kang, J. G. Lee, J. Y. An, H. S. Youn, K. R. Park, T. G. Kim, J. K. Yang, Y. Jun, S. H. Eom
Structural Insights Into The Interaction Of P97 N-Terminus Domain And Vbm In Rhomboid Protease, Rhbdl4.
Biochem. J. V. 473 2863 2016
PubMed-ID: 27407164  |  Reference-DOI: 10.1042/BCJ20160237

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    ChainsA
    EC Number3.6.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 21-199
    GeneVCP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING PROTEIN,VCP
 
Molecule 2 - RHOMBOID-RELATED PROTEIN 4
    ChainsB
    EC Number3.4.21.105
    EngineeredYES
    FragmentVBM MOTIF (RESIDUES 300-314)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRRP4,RHOMBOID DOMAIN-CONTAINING PROTEIN 1,RHOMBOID-LIKE PROTEIN 4
    SyntheticYES

 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 5EPP)

(-) Sites  (0, 0)

(no "Site" information available for 5EPP)

(-) SS Bonds  (0, 0)

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

(-) 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 5EPP)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5EPP)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeeehhhhhhhh......eeeee.....eeeeeeee.......eeeehhhhhhhhh.....eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5epp A  21 NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIK 190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5epp B 300 SPEEMRRQRLHRFDS 314
                                   309     

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  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 5EPP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (96, 102)

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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 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 5b6c 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifs 5ifw 5x4l

(-) Related Entries Specified in the PDB File

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