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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY RPN13 PRU-RPN2 (940-953)-UBIQUITIN COMPLEX
 
Authors :  C. W. Hemmis, R. T. Vanderlinden, T. Yao, H. Robinson, C. P. Hill
Date :  02 Mar 17  (Deposition) - 03 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Rpn13, Proteasome, Rpn2, Ubiquitin, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. T. Vanderlinden, C. W. Hemmis, T. Yao, H. Robinson, C. P. Hill
Structure And Energetics Of Pairwise Interactions Between Proteasome Subunits Rpn2, Rpn13, And Ubiquitin Clarify A Substrate Recruitment Mechanism.
J. Biol. Chem. V. 292 9493 2017
PubMed-ID: 28442575  |  Reference-DOI: 10.1074/JBC.M117.785287

(-) Compounds

Molecule 1 - PROTEASOMAL UBIQUITIN RECEPTOR ADRM1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET151
    Expression System StrainBL21 RIL
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentPRU DOMAIN (UNP RESIDUES 19-132)
    GeneADRM1, GP110
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ADHESION- REGULATING MOLECULE 1, ARM-1, PROTEASOME REGULATORY PARTICLE NON- ATPASE 13, HRPN13, RPN13 HOMOLOG
 
Molecule 2 - UBIQUITIN
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET3A
    Expression System StrainBL21 RIL
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneUBB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 1
    ChainsE, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET151
    Expression System StrainBL21 RIL
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentC-TERMIMAL DOMAIN (UNP RESIDUES 940-953)
    GenePSMD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym26S PROTEASOME REGULATORY SUBUNIT RPN2, 26S PROTEASOME REGULATORY SUBUNIT S1, 26S PROTEASOME SUBUNIT P112, RPN2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A C E 
Biological Unit 2 (1x) B D F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5V1Y)

(-) Sites  (0, 0)

(no "Site" information available for 5V1Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V1Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V1Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5V1Y)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeee....eeeeeee.....eeeeeee.....eeeeeee....eeeee........eeeeee.....eeeeee......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5v1y A  18 PSNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNP 131
                                    27        37        47        57        67        77        87        97       107       117       127    

Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee..eeee....eeeeeee.....eeeeeee.....eeeeeee....eeeee........eeeeee.....eeeeee......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5v1y B  20 NKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFPDDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNPP 132
                                    29        39        49        59        69        79        89        99       109       119       129   

Chain C from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5v1y C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  72
                                    10        20        30        40        50        60        70  

Chain D from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5v1y D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

Chain E from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author ..........ee.. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5v1y E 938 GPQEPEPPEPFEYI 951
                                   947    

Chain F from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .........ee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5v1y F 939 PQEPEPPEPFEY 950
                                   948  

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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 5V1Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V1Y)

(-) Gene Ontology  (107, 133)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADRM1_HUMAN | Q161862kqz 2kr0 2l5v 2mkz 2nbk 2nbv 4uel 4uem 4wlq 4wlr 5irs 5v1z
        PSMD1_HUMAN | Q994602nbk 5gjq 5gjr 5l4k 5ln3 5m32 5t0c 5t0g 5t0h 5t0i 5t0j 5v1z
        UBB_HUMAN | P0CG471c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

5v1z