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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UBX DOMAIN OF HUMAN UBXD7 IN COMPLEX WITH P97 N DOMAIN
 
Authors :  T. Jiang, Z. Li, Y. Wang, M. Xu
Date :  13 Feb 17  (Deposition) - 22 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Ubxd7, P97, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. H. Li, Y. Wang, M. Xu, T. Jiang
Crystal Structures Of The Ubx Domain Of Human Ubxd7 And Its Complex With P97 Atpase
Biochem. Biophys. Res. V. 486 94 2017 Commun.
PubMed-ID: 28274878  |  Reference-DOI: 10.1016/J.BBRC.2017.03.005

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    ChainsA, B
    EC Number3.6.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 23-196
    GeneVCP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTER ATPASE,15S MG(2+)-ATPASE P97 SUBUNIT,VALOSIN-CONTAINING PROTEIN,VCP
 
Molecule 2 - UBX DOMAIN-CONTAINING PROTEIN 7
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 410-489
    GeneUBXN7, KIAA0794, UBXD7
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5X4L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X4L)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:169 -Pro A:170
2Ser A:171 -Pro A:172
3Asp B:169 -Pro B:170
4Ser B:171 -Pro B:172
5Phe C:458 -Pro C:459
6Cys C:478 -Pro C:479
7Phe D:458 -Pro D:459
8Cys D:478 -Pro D:479

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X4L)

(-) Exons   (0, 0)

(no "Exon" information available for 5X4L)

(-) 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 ...eeeee........eeeehhhhhhhh......eeeee.....eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeee......eeeeeeeee...eeee....eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x4l A  22 SPNRLIVDEAINEDNSVVSLSQPKmDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRmNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGmRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKR 191
                                    31        41    |   51        61        71        81  |     91       101       111       121       131       141       151      |161       171       181       191
                                                   46-MSE                                84-MSE                                                                   158-MSE                             

Chain B from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........eeeehhhhhhhh......eeeee.....eeeeeeee.......eeeehhhhhhhhh.....eeeeee........eeeeee.hhhh.....hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5x4l B  24 NRLIVDEAINEDNSVVSLSQPKmDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRmNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGmRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKR 191
                                    33        43  |     53        63        73        83|       93       103       113       123       133       143       153    |  163       173       183        
                                                 46-MSE                                84-MSE                                                                   158-MSE                             

Chain C from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee...hhhhhhhhhhhh......eeeee....ee.hhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 5x4l C 411 PKAQLmLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITmQEAGLCPQETVFVQERN 489
                                 | 420       430       440       450       460       470 |     480         
                               416-MSE                                                 472-MSE             

Chain D from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee...hhhhhhhhhhhh......eeeee....ee.hhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 5x4l D 411 PKAQLmLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITmQEAGLCPQETVFVQERN 489
                                 | 420       430       440       450       460       470 |     480         
                               416-MSE                                                 472-MSE             

   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 5X4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X4L)

(-) Gene Ontology  (74, 79)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:169 - Pro A:170   [ RasMol ]  
    Asp B:169 - Pro B:170   [ RasMol ]  
    Cys C:478 - Pro C:479   [ RasMol ]  
    Cys D:478 - Pro D:479   [ RasMol ]  
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    Phe D:458 - Pro D:459   [ 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 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifs 5ifw
        UBXN7_HUMAN | O948881wj4 2dal 2dlx 5x3p

(-) Related Entries Specified in the PDB File

5x3p