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(-) Description

Title :  1.65 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA
 
Authors :  M. Simonovic, P. G. W. Gettins, K. Volz
Date :  26 Jul 02  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Serpin, Crma, Apoptosis, Ice Inhibitor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Simonovic, P. G. W. Gettins, K. Volz
Crystal Structure Of Viral Serpin Crma Provides Insights Into Its Mechanism Of Cysteine Proteinase Inhibition
Protein Sci. V. 9 1423 2000
PubMed-ID: 10975564
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEINASE INHIBITOR 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-60
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Fragment: RESIDUES 1-55
    Gene: CRMA
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243
    Synonym: CYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN
 
Molecule 2 - SERINE PROTEINASE INHIBITOR 2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-60
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Fragment: RESIDUES 56-300
    Gene: CRMA
    Mutation: YES
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243
    Synonym: CYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN
 
Molecule 3 - SERINE PROTEINASE INHIBITOR 2
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-60
    Expression System Strain: SG13009
    Expression System Taxid: 562
    Fragment: RESIDUES 301-341
    Gene: CRMA
    Mutation: YES
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243
    Synonym: CYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , ASP A:2 , ARG A:5 , HOH A:566 , THR B:215 , ASP B:216BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M93)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M93)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPI2_CWPXB312-322  1C:312-322

(-) Exons   (0, 0)

(no "Exon" information available for 1M93)

(-) 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:46
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:46
                                    10        20        30        40      
           SPI2_CWPXB     1 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYV  46
               SCOP domains d1m93.1 A:,B:,C:                               SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1m93 A   1 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYV  46
                                    10        20        30        40      


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:245
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     
           SPI2_CWPXB    56 DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDCRTVDAINKCVDIFTEGKINPLLDEPLSPDTCLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWCDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMCNSDVSVDAMIHKTYIDVNEEYTEAAAATCAL 300
               SCOP domains d1m93.1 A:,B:,C: Viral serpin crmA (cytokine response modifier protein)                                                                                                                                                                               SCOP domains
               CATH domains 1m93B01 B:56-132,B:241-283,B:294-300 Antithrombin, subunit I, domain 2       1m93B02 B:133-240,B:284-293 Alpha-1-antitrypsin, domain 1                                                   1m93B01 B:56-132,B:241-283,B:294-300       1m93B02   1m93B01 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....hhhhhhhhh..eeee....hhhhhhhhhhhhhhh.................eeeeeeeeeeee.....hhhhheeeeeeee..eeeeeeeeee...eeeeeee......eeeeeee....eeeeeeee....hhhhhhh..hhhhhhhhhhh.eeee.eeeee.eeeeeeeehhhhhhhh........................eeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m93 B  56 DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDSRTVDAINKSVDIFTEGKINPLLDEPLSPDTSLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWSDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMSNSDVSVDAMIHKTYIDVNEEYTEAAAATSAL 300
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     


Chain C from PDB  Type:PROTEIN  Length:31
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:31
                                   318       328       338 
           SPI2_CWPXB   309 TNEFCADHPFIYVIRHVDGKILFVGRYCSPT 339
               SCOP domains d1m93.1 A:,B:,C:                SCOP domains
               CATH domains ------------------------------- CATH domains
           Pfam domains (1) Serpin-1m93C01 C:309-338      - Pfam domains (1)
           Pfam domains (2) Serpin-1m93C02 C:309-338      - Pfam domains (2)
           Pfam domains (3) Serpin-1m93C03 C:309-338      - Pfam domains (3)
         Sec.struct. author ..eee....eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ---SERPIN     ----------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1m93 C 309 TNEFSADHPFIYVIRHVDGKILFVGRYSSPT 339
                                   318       328       338
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Serpin] (63)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SPI2_CWPXB | P07385)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0039650    suppression by virus of host cysteine-type endopeptidase activity involved in apoptotic process    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host caspase activity. Caspases are cysteine-type endopeptidases which contribute to the apoptotic process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPI2_CWPXB | P07385: 1c8o 1f0c

(-) Related Entries Specified in the PDB File

1c8o 1C8O IS THE 2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA
1f0c 1F0C IS THE STRUCTURE OF THE VIRAL SERPIN CRMA