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(-) Description

Title :  CRYSTAL STRUCTURE OF P97/VCP N IN COMPLEX WITH OTU1 UBXL
 
Authors :  S. J. Kim, E. E. Kim
Date :  25 Apr 13  (Deposition) - 19 Mar 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Aaa Atpase, Ubx-Like Domain, Protein Binding, Protein-Protein Complex, Beta-Barrel, Beta-Grasp, Signaling Protein-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Kim, J. Cho, E. J. Song, S. J. Kim, H. M. Kim, K. E. Lee, S. W. Suh, E. E. Kim
Structural Basis For Ovarian Tumor Domain-Containing Protei 1 (Otu1) Binding To P97/Valosin-Containing Protein (Vcp).
J. Biol. Chem. V. 289 12264 2014
PubMed-ID: 24610782  |  Reference-DOI: 10.1074/JBC.M113.523936

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    Chains: A
    EC Number: 3.6.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N DOMAIN (RESIDUES 23-196)
    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 - UBIQUITIN THIOESTERASE OTU1
    Chains: B
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UBX-LIKE DOMAIN (RESIDUES 1-73)
    Gene: OTU1, YFL044C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: OTU DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4KDL)

(-) Sites  (0, 0)

(no "Site" information available for 4KDL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KDL)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:169 -Pro A:170
2Ser A:171 -Pro A:172
3Tyr B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KDL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KDL)

(-) Exons   (0, 0)

(no "Exon" information available for 4KDL)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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 d4kdla1 A:23-106 Membrane fusion ATPase p97 N-terminal domain , P97-Nn              d4kdla2 A:107-196 Membrane fusion atpase p97 domain 2, P97-Nc                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........eeeehhhhhhhh......eeeee.....eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeeehhhhhh....hhhhhhhhhhhh...eeee...eeee......eeeeeeeee...eeee....eee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kdl A  23 PNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEE 196
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    


Chain B from PDB  Type:PROTEIN  Length:69
                                                                                                     
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....hhhhhhhhh.....eeee....eeee.hhhhh.hhhhh....eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4kdl B   0 SMKLKVTGAGINQVVTLKQDATLNDLIEHINVDVKTMRFGYPPQRINLSLGQTQLDELGINSGEKITIE  73
                                     9        19        29        39       |54        64         
                                                                          47|                    
                                                                           53
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KDL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KDL)

(-) Gene Ontology  (80, 83)

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  Cis Peptide Bonds
    Asp A:169 - Pro A:170   [ RasMol ]  
    Ser A:171 - Pro A:172   [ RasMol ]  
    Tyr B:40 - Pro B:41   [ RasMol ]  
 
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  4kdl
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  TERA_HUMAN | P55072
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 Related Entries

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

UniProtKB/Swiss-Prot
        OTU1_YEAST | P43558: 3by4 3c0r 4kdi
        TERA_HUMAN | P55072: 3ebb 3hu1 3hu2 3hu3 3qc8 3qq7 3qq8 3qwz 3tiw 4kdi 4kln 4ko8 4kod 4p0a 5b6c 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifs 5ifw 5x4l

(-) Related Entries Specified in the PDB File

4kdi CRYSTAL STRUCTURE OF P97/VCP N IN COMPLEX WITH OTU1 UBXL