Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CMR6 FROM PYROCOCCUS FURIOSUS
 
Authors :  C. Benda, J. Ebert, M. Baumgaertner, E. Conti
Date :  26 Aug 14  (Deposition) - 15 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cmr Complex, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Benda, J. Ebert, R. A. Scheltema, H. B. Schiller, M. Baumgartner, F. Bonneau, M. Mann, E. Conti
Structural Model Of A Crispr Rna-Silencing Complex Reveals The Rna-Target Cleavage Activity In Cmr4.
Mol. Cell V. 56 43 2014
PubMed-ID: 25280103  |  Reference-DOI: 10.1016/J.MOLCEL.2014.09.002

(-) Compounds

Molecule 1 - CRISPR SYSTEM CMR SUBUNIT CMR6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 101-340
    Gene: CMR6, PF1124
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: CRISPR TYPE III-B/RAMP MODULE RAMP PROTEIN CMR6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4W8V)

(-) Sites  (0, 0)

(no "Site" information available for 4W8V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W8V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:274 -Pro A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W8V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W8V)

(-) Exons   (0, 0)

(no "Exon" information available for 4W8V)

(-) 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
(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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...eeee....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhh........ee...ee.hhhh......eeeeeeeeee.....................eeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w8v A 102 MLNSLHAITGKFKTQSRLVVGLGDESVYETSIRLLRNYGVPYIPGSAIKGVTRHLTYYVLAEFINNDFYKRAKTVQDAFMKGDPKEILSNAKVPERCSRLCKEFLRIFGEKKVPEIIDELIRIFGTQKKEGEVVFFDAIPIAEEIADKPILELDIMNPHYGPYYQSGEKNVPPPGDWYDPIPIFFLTVPKDVPFLVAVGGRDRELTEKAFSLVKLALRDLGVGAKTSLGYGRLVEYV 340
                                   111       121       131       141       151       161    || 173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       
                                                                                          166|                                                                                                                                                                           
                                                                                           169                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eeee....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhh.......eee...ee.hhhh......eeeeeeeeee..................eeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w8v B 102 MLSLHAITGKFKTQSRLVVGLGDESVYETSIRLLRNYGVPYIPGSAIKGVTRHLTYYVLAEFINNDFYKRAKTVQDAFMKGDPKEILSNAKVPERCSRLCKEFLRIFGEKKVPEIIDELIRIFGTQKKEGEVVFFDAIPIAEEIADKPILELDIMNPHYGPYYQSGVPPPGDWYDPIPIFFLTVPKDVPFLVAVGGRDRELTEKAFSLVKLALRDLGVGAKTSLGYGRLVEY 339
                             ||    112       122       132       142       152       162   ||  174       184       194       204       214       224       234       244       254       264     ||277       287       297       307       317       327       337  
                           103|                                                          166|                                                                                                  270|                                                                 
                            105                                                           169                                                                                                   274
   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  (0, 0)

(no "SCOP Domain" information available for 4W8V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W8V)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 4w8v)
 
  Sites
(no "Sites" information available for 4w8v)
 
  Cis Peptide Bonds
    Val A:274 - Pro A:275   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4w8v
    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
  CMR6_PYRFU | Q8U1T1
    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
  CMR6_PYRFU | Q8U1T1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4W8V)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4W8V)