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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE INTERACTION OF P97 N-TERMINAL DOMAIN AND SHP MOTIF IN DERLIN-1 RHOMBOID PSEUDOPROTEASE
 
Authors :  J. J. Lim, Y. Lee, S. Y. Yoon, T. T. Ly, J. Y. Kang, H. -S. Youn, J. Y. An, J. -G K. R. Park, T. G. Kim, J. K. Yang, Y. Jun, S. H. Eom
Date :  11 Jul 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Beta-Barrel, Atpase, Derlin1 Shp Box Ubiquitin, Phosphorylation, Hydrolase-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Lim, Y. Lee, S. Y. Yoon, T. T. Ly, J. Y. Kang, H. S. Youn, J. Y. An, J. G. Lee, K. R. Park, T. G. Kim, J. K. Yang, Y. Jun, S. H. Eom
Structural Insights Into The Interaction Of Human P97 N-Terminal Domain And Shp Motif In Derlin-1 Rhomboid Pseudoprotease.
Febs Lett. 2016
PubMed-ID: 27714797  |  Reference-DOI: 10.1002/1873-3468.12447

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    Chains: A, C, E, G
    EC Number: 3.6.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: P97 N-TERMINAL DOMAIN (UNP RESIDUES 21-199)
    Gene: VCP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING PROTEIN,VCP
 
Molecule 2 - DERLIN-1
    Chains: B, D, F, H
    Engineered: YES
    Fragment: SHP BOX (UNP RESIDUES 239-250)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEGRADATION IN ENDOPLASMIC RETICULUM PROTEIN 1,DERTRIN-1, DER1-LIKE PROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5GLF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Asp A:169 -Pro A:170
2Ser A:171 -Pro A:172
3Thr C:127 -Gly C:128
4Asp C:169 -Pro C:170
5Ser C:171 -Pro C:172
6Glu E:124 -Gly E:125
7Asp E:169 -Pro E:170
8Ser E:171 -Pro E:172
9Asp G:169 -Pro G:170
10Ser G:171 -Pro G:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GLF)

(-) 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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eee.hhhhhhhhh.....eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5glf A  23 PNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRE 192
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ......eee... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5glf B 239 RHNWGQGFRLGD 250
                                   248  


Chain C from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeee...hhhhh..hhhhhhhhhhhh...eeee...eeee......eeeeeeeee...eeee....eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5glf C  22 RPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRE 192
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....eee... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5glf D 240 HNWGQGFRLGD 250
                                   249 


Chain E from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eee.hhhhhhhhh.....eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeeee....eeeeeeeeee...eeee....eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5glf E  24 NRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKRE 192
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183         


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....eee.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5glf F 240 HNWGQGFRLG 249
                                   249


Chain G from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5glf G  23 PNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIK 190
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182        


Chain H from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....eee.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5glf H 240 HNWGQGFRLG 249
                                   249
   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 5GLF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (90, 106)

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  Cis Peptide Bonds
    Asp A:169 - Pro A:170   [ RasMol ]  
    Asp C:169 - Pro C:170   [ RasMol ]  
    Asp E:169 - Pro E:170   [ RasMol ]  
    Asp G:169 - Pro G:170   [ RasMol ]  
    Glu E:124 - Gly E:125   [ RasMol ]  
    Ser A:171 - Pro A:172   [ RasMol ]  
    Ser C:171 - Pro C:172   [ RasMol ]  
    Ser E:171 - Pro E:172   [ RasMol ]  
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  5glf
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 Related Entries

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        TERA_HUMAN | P55072: 3ebb 3hu1 3hu2 3hu3 3qc8 3qq7 3qq8 3qwz 3tiw 4kdi 4kdl 4kln 4ko8 4kod 4p0a 5b6c 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5ifs 5ifw 5x4l

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