Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE VIRAL SERPIN CRMA
 
Authors :  M. Renatus, Q. Zhou, H. R. Stennicke, S. J. Snipas, D. Turk, L. A. Bankston, R. C. Liddington, G. S. Salvesen
Date :  15 May 00  (Deposition) - 06 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apoptosis, Caspase Inhibitor, Protease Inhibitor, Serpin, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Renatus, Q. Zhou, H. R. Stennicke, S. J. Snipas, D. Turk, L. A. Bankston, R. C. Liddington, G. S. Salvesen
Crystal Structure Of The Apoptotic Suppressor Crma In Its Cleaved Form.
Structure Fold. Des. V. 8 789 2000
PubMed-ID: 10903953  |  Reference-DOI: 10.1016/S0969-2126(00)00165-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ICE INHIBITOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-305
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243
    Synonym: CYTOKINE RESPONSE MODIFIER PROTEIN, CRMA
 
Molecule 2 - ICE INHIBITOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 306-341
    Organism Scientific: COWPOX VIRUS
    Organism Taxid: 10243
    Synonym: CYTOKINE RESPONSE MODIFIER PROTEIN, CRMA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:258 , LEU A:260 , PRO B:369 , CYS B:389BINDING SITE FOR RESIDUE DTT A 360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F0C)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:170 -Pro A:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F0C)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPI2_CWPXB312-322  1B:364-374

(-) Exons   (0, 0)

(no "Exon" information available for 1F0C)

(-) 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:297
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
          SPI2_CWPXB      1 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYVEKEADKNKDDISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDCRTVDAINKCVDIFTEGKINPLLDEPLSPDTCLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWCDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMCNSDVSVDAMIHKTYIDVNEEYTEAAAATCALVADCA  305
               SCOP domains d1f0c.1 A:,B: Viral serpin crmA (cytokine respo        nse modifier protein)                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------1f0cA01 A:51-189,A:294-337,A:34        8-358 Antithrombin, subunit I, domain 2                                      1f0cA02 A:190-293,A:338-347 Alpha-1-antitrypsin, domain 1                                                   1f0cA01 A:51-189,A:294-337,A:348-358       1f0cA02   1f0cA01    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....eeehhhhhhhhhhhhhhhh.hhhhhhhhh...--------...eeeeeeeeee.....hhhhhhhhh..eeee....hhhhhhhhhhhhhhh...............eeeeeeeeeeeeee.....hhhhheeeeeeee..eeeeeeeeeeeeeeeeeeee......eeeeeee....eeeeeeee....hhhhhhh..hhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhh....................eeeeeeeeeeeee...eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f0c A   35 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYVE--------DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDCRTVDAINKCVDIFTEGKINPLLDEPLSPDTCLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWCDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMCNSDVSVDAMIHKTYIDVNEEYTEAAAATCALVADCA  359
                                    44        54        64        74      |  -     ||113       123       133  ||   147||     158       168       179||     187       197       207       217       226      235A|      244       254   |   263       273       283       293       303       313       324       334       344       354     
                                                                         81      103|                       136|    148|                       176| ||                                          224A        235A|                   257A                                                              322|                                   
                                                                                  110                        141     150                        178 ||                                                       235B                                                                                      324                                   
                                                                                                                                                 179A|                                                                                                                                                                                       
                                                                                                                                                  179B                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:36
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:36
                                   315       325       335      
          SPI2_CWPXB    306 STVTNEFCADHPFIYVIRHVDGKILFVGRYCSPTTN  341
               SCOP domains d1f0c.1 A:,B:                        SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .....eee....eeeeeee....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------SERPIN     ------------------- PROSITE
                 Transcript ------------------------------------ Transcript
                1f0c B 359A STVTNEFCADHPFIYVIRHVDGKILFVGRYCSPTTN  394
                            ||     367       377||     388      
                         359A|                378|              
                          359B                 380
   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  (0, 0)

(no "Pfam Domain" information available for 1F0C)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DTT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:170 - Pro A:171   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1f0c
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPI2_CWPXB | P07385
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SPI2_CWPXB | P07385
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPI2_CWPXB | P07385: 1c8o 1m93

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1F0C)