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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MIDDLE-EAST RESPIRATORY SYNDROME CORONAVIRUS PAPAIN-LIKE PROTEASE IN COMPLEX WITH UBIQUITIN (SPACE GROUP P6522)
 
Authors :  B. A. Bailey-Elkin, G. G. Johnson, B. L. Mark
Date :  24 Sep 14  (Deposition) - 22 Oct 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Zinc Ribbon, Deubiquitinase, Papain-Like Protease, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Bailey-Elkin, R. C. Knaap, G. G. Johnson, T. J. Dalebout, D. K. Ninaber, P. B. Van Kasteren, P. J. Bredenbeek, E. J. Snijder, M. Kikkert, B. L. Mark
Crystal Structure Of The Middle East Respiratory Syndrome Coronavirus (Mers-Cov) Papain-Like Protease Bound To Ubiquitin Facilitates Targeted Disruption Of Deubiquitinating Activity To Demonstrate Its Role In Innate Immune Suppression.
J. Biol. Chem. V. 289 34667 2014
PubMed-ID: 25320088  |  Reference-DOI: 10.1074/JBC.M114.609644

(-) Compounds

Molecule 1 - ORF1AB PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1480-1803
    GeneORF1AB
    Organism ScientificHUMAN BETACORONAVIRUS 2C JORDAN-N3/2012
    Organism Taxid1306931
 
Molecule 2 - UBIQUITIN-60S RIBOSOMAL PROTEIN L40
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-75
    GeneUBA52, UBCEP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCEP52, UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION PRODUCT 1, UBIQUITIN, 60S RIBOSOMAL PROTEIN L40

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
13CN1Ligand/Ion3-AMINOPROPANE
2SO49Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1672 , CYS A:1675 , CYS A:1707 , CYS A:1709BINDING SITE FOR RESIDUE ZN A 1901
02AC2SOFTWAREASN A:1673 , HIS A:1714 , HIS A:1759BINDING SITE FOR RESIDUE SO4 A 1902
03AC3SOFTWAREGLN A:1751 , GLY A:1752 , LYS A:1787BINDING SITE FOR RESIDUE SO4 A 1903
04AC4SOFTWAREGLU A:1659 , LEU A:1660 , GLY A:1684 , LEU A:1685 , LYS A:1686BINDING SITE FOR RESIDUE SO4 A 1904
05AC5SOFTWARETRP A:1668 , GLU A:1670 , ARG A:1715 , ALA B:46BINDING SITE FOR RESIDUE SO4 A 1905
06AC6SOFTWAREHIS A:1652 , LEU A:1655 , ALA A:1656 , LYS A:1686 , CYS A:1689 , HOH A:2002 , LYS B:48BINDING SITE FOR RESIDUE SO4 A 1906
07AC7SOFTWAREVAL A:1582 , ASP A:1602 , ARG A:1764BINDING SITE FOR RESIDUE SO4 A 1907
08AC8SOFTWAREPHE A:1515 , TYR A:1565 , LYS A:1568BINDING SITE FOR RESIDUE SO4 A 1908
09AC9SOFTWAREASN A:1590 , CYS A:1592 , ASN A:1673 , GLY A:1758 , HIS A:1759 , GLY B:75BINDING SITE FOR RESIDUE 3CN B 101
10BC1SOFTWARETYR A:1705 , ARG A:1715 , THR B:66 , HIS B:68BINDING SITE FOR RESIDUE SO4 B 102
11BC2SOFTWAREGLN B:31 , ASP B:39 , ARG B:72 , ARG B:74BINDING SITE FOR RESIDUE SO4 B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RF0)

(-) Exons   (0, 0)

(no "Exon" information available for 4RF0)

(-) 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    
   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:318
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeeee....hhhhhh......................eee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eee....eee.....hhhhhhhhhhhh....eee.hhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhh.eee....eeeeeeee...eeeeeeee.hhh.eee...hhhhhhh.eeee.....eeeeeeeeeee..eeeeeeeeeeeee........eeeeee.......eeeeeeee..eeeee....ee...eeeeeeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4rf0 A 1484 TIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSD 1801
                                  1493      1503      1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613      1623      1633      1643      1653      1663      1673      1683      1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793        

Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                            
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee...............eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                4rf0 B    1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75
                                    10        20        30        40        50        60        70     

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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 4RF0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RF0)

(-) Gene Ontology  (124, 124)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_HUMAN | P629871c3t 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 2lj5 2mbh 2mjb 2mur 2n3u 2n3v 2n3w 2nbd 2nbe 2nr2 2o6v 2ojr 2pe9 2pea 2rsu 2w9n 2wdt 2xew 2xk5 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 3phd 4hjk 4jio 4p4h 4pig 4pih 4pij 4rf1 4s1z 4ug0 4v6x 4xkl 5aj0 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5hpk 5hpl 5hps 5hpt 5j26 5j8p 5jbv 5jby 5t2c
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        M4STU1_9BETC | M4STU14rez 4rf1

(-) Related Entries Specified in the PDB File

4rez 4rf1