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 :  MRE11 ATLD17/18 MUTATION RETAINS TEL1/ATM ACTIVITY BUT BLOCKS DNA DOUBLE-STRAND BREAK REPAIR
 
Authors :  O. Limbo, D. Moiani, A. Kertokalio, C. Wyman, J. A. Tainer, P. Russell
Date :  01 Oct 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclease Enzyme, Double-Strand Break Repair, Rad50, Nbs1, Mutation L204R, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Limbo, D. Moiani, A. Kertokalio, C. Wyman, J. A. Tainer, P. Russell
Mre11 Atld17/18 Mutation Retains Tel1/Atm Activity But Blocks Dna Double-Strand Break Repair.
Nucleic Acids Res. V. 40 11435 2012
PubMed-ID: 23080121  |  Reference-DOI: 10.1093/NAR/GKS954

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PFMRE11
    Gene: MRE11, PF1166
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1
    Synonym: PFMRE11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:49 , ASN A:84 , HIS A:173 , HIS A:206 , MN A:402BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREASP A:8 , HIS A:10 , ASP A:49 , HIS A:208 , MN A:401BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREASP B:8 , HIS B:10 , ASP B:49 , HIS B:208 , MN B:402BINDING SITE FOR RESIDUE MN B 401
4AC4SOFTWAREASP B:8 , ASP B:49 , ASN B:84 , HIS B:173 , HIS B:206 , MN B:401BINDING SITE FOR RESIDUE MN B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HD0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp A:186 -Tyr A:187
2Thr B:88 -Gln B:89
3Ile B:285 -Arg B:286
4Arg B:286 -Lys B:287
5Lys B:287 -Ala B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HD0)

(-) Exons   (0, 0)

(no "Exon" information available for 4HD0)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4hd0a_ A: Mre11                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhh...eee............hhhhhhhhh...ee.eee........eeeee.....eeeeeee..eeeeee............hhhhhhh.....eeeeee..hhhhhhhh.......hhhhh.....eeeee.....eeeee..eeeee.......hhhhh.eeeee....eeeee....eeeeee..eeeeee.....eeeeee...hhhhhhhhhhhhhhh....eeeeeeee.....hhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hd0 A   1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYARGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWR 332
                                    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       310       320       330  


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4hd0b_ B: Mre11                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhh...eee............hhhhhhhhh...ee.eee........eeeee.....eeeeeee..eeeeee...hhhhhh...hhhhhhh.....eeeeee........hhhhh.....eeeee.....eeeee..eeeee.......hhhhh.eeeee....ee......eeeeeee..eeeeeee....eeeee..........hhhhh....eeeee........hhhhhhhhh..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hd0 B   1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREFEIGLGDLPEGYLYYARGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWR 332
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       189       199       209       219       229       239       249       259       269       279|      293       303       313       323         
                                                                                                                                                                                                           178|                                                                                        279|                                                
                                                                                                                                                                                                            188                                                                                         284
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HD0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HD0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg B:286 - Lys B:287   [ RasMol ]  
    Asp A:186 - Tyr A:187   [ RasMol ]  
    Ile B:285 - Arg B:286   [ RasMol ]  
    Lys B:287 - Ala B:288   [ RasMol ]  
    Thr B:88 - Gln B:89   [ 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
  4hd0
    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
  MRE11_PYRFU | Q8U1N9
    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
  MRE11_PYRFU | Q8U1N9
    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
        MRE11_PYRFU | Q8U1N9: 1ii7 1s8e 3dsc 3dsd 3qkr 3qks 3qku

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HD0)