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(-) Description

Title :  CRYSTAL STRUCTURE OF SARS-COV PAPAIN-LIKE PROTEASE C112S MUTANT IN COMPLEX WITH UBIQUITIN
 
Authors :  C. -Y. Chou, H. -Y. Chen, H. -Y. Lai, S. -C. Cheng, Y. -W. Chou
Date :  02 Aug 13  (Deposition) - 12 Feb 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Papain-Like Protease-Ubiquitin Complex, Protein Hydrolase And Deubiquitination, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -Y. Chou, H. -Y. Lai, H. -Y. Chen, S. -C. Cheng, K. -W. Cheng, Y. -W. Cho
Structural Basis For Catalysis And Ubiquitin Recognition By The Severe Acute Respiratory Syndrome Coronavirus Papain-Like Protease
Acta Crystallogr. , Sect. D V. 70 572 2014
PubMed-ID: 24531491  |  Reference-DOI: 10.1107/S1399004713031040

(-) Compounds

Molecule 1 - REPLICASE POLYPROTEIN 1A
    Chains: A
    EC Number: 3.4.19.12, 3.4.22.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NSP3 PAPAIN-LIKE PROTEASE DOMAIN, UNP RESIDUES 1541-1858
    Gene: 1A, NSP3
    Mutation: YES
    Organism Common: SARS-COV
    Organism Scientific: SARS CORONAVIRUS
    Organism Taxid: 227859
 
Molecule 2 - UBIQUITIN
    Chains: B
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Tissue: ERYTHROCYTES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:190 , CYS A:193 , CYS A:225 , CYS A:227BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARESER A:112 , SER A:115 , SER A:116 , TYR A:274 , HOH A:702BINDING SITE FOR RESIDUE NA A 402
3AC3SOFTWARELYS A:106 , TRP A:107 , ASP A:287 , GLY A:288 , ALA A:289 , HIS A:290 , THR A:313 , ILE A:315 , HOH A:520 , HOH A:561 , HOH A:742BINDING SITE FOR RESIDUE NHE A 403
4AC4SOFTWAREGLN A:123 , LEU A:124 , GLU A:125 , ARG A:141 , HOH A:703BINDING SITE FOR RESIDUE NHE A 404
5AC5SOFTWAREHIS A:18 , GLN A:20 , ASP A:62 , THR A:64 , LEU A:65 , HOH A:639BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWARETYR A:252 , LYS A:253 , LEU A:254 , GLN A:255 , THR A:258 , TYR A:306BINDING SITE FOR RESIDUE GOL A 406
7AC7SOFTWAREGLU B:24 , ASN B:25 , ALA B:28BINDING SITE FOR RESIDUE GOL B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M0W)

(-) Exons   (0, 0)

(no "Exon" information available for 4M0W)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeeee...hhhhhh..eee..ee......hhhhh..eeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.....ee..ee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhh.......eeeeeeee...eeeeeeee.hhh.eee...hhhhhhhheeee.....eeeeeeeeee..eeeeeeeeeeeeee.....eeeeeee....eeeeeeee...eeeee..eeeee.eeeeeeeeeeee..eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m0w A   3 VKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNSYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVS 319
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains d4m0wb_ B: Ubiquitin                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4m0w B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M0W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M0W)

(-) Gene Ontology  (43, 44)

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
        R1A_CVHSA | P0C6U8: 1o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2kaf 2kqv 2kqw 2kys 2liz 2op9 2ozk 2pwx 2q6g 2qc2 2qcy 2qiq 2rhb 2rnk 2w2g 2wct 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 2zu4 2zu5 3atw 3avz 3aw0 3aw1 3d62 3e91 3e9s 3ea7 3ea8 3ea9 3eaj 3ee7 3f9e 3f9f 3f9g 3f9h 3fzd 3iwm 3m3s 3m3t 3m3v 3mj5 3r24 3sn8 3sna 3snb 3snc 3snd 3sne 3szn 3tit 3tiu 3tns 3tnt 3v3m 3vb3 3vb4 3vb5 3vb6 3vb7 4hi3 4mds 4mm3 4ovz 4ow0 5f22
        RS27A_BOVIN | P62992: 1aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2fif 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4y1h 4z9s 5bz0 5fer 5jqs 5mn9

(-) Related Entries Specified in the PDB File

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