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 ATPRS-MRE11/RAD50-DNA COMPLEX
 
Authors :  Y. Liu
Date :  10 Sep 15  (Deposition) - 24 Feb 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Nuclease, Recombination-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, S. Sung, Y. Kim, F. Li, G. Gwon, A. Jo, A. K. Kim, T. Kim, O. K. Song, S. E. Lee, Y. Cho
Atp-Dependent Dna Binding, Unwinding, And Resection By The Mre11/Rad50 Complex.
Embo J. V. 35 743 2016
PubMed-ID: 26717941  |  Reference-DOI: 10.15252/EMBJ.201592462

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MRE11, MJ1323
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
 
Molecule 2 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE,DNA DOUBLE- STRAND BREAK REPAIR RAD50 ATPASE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-190, 825-1005
    Gene: RAD50, MJ1322
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
 
Molecule 3 - DNA (27-MER)
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: DNA A1
    Synthetic: YES
 
Molecule 4 - DNA (27-MER)
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: DNA A2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , ASP A:49 , HIS A:188 , MG A:402binding site for residue MG A 401
2AC2SOFTWAREASP A:49 , ASN A:84 , HIS A:158 , HIS A:186 , MG A:401binding site for residue MG A 402
3AC3SOFTWARELYS B:14 , SER B:15 , GLY B:35 , SER B:36 , GLY B:37 , LYS B:38 , SER B:39 , SER B:40 , THR B:60 , ILE B:62 , THR B:63 , LYS B:64 , GLN B:134 , ASP B:946 , GLU B:947 , LYS B:994 , TYR D:890 , LEU D:910 , ASN D:914 , SER D:916 , GLU D:919binding site for residue AGS B 1101
4AC4SOFTWAREASP C:49 , ASN C:84 , HIS C:158 , HIS C:186 , MG C:402binding site for residue MG C 401
5AC5SOFTWAREASP C:8 , HIS C:10 , ASP C:49 , HIS C:188 , MG C:401 , HOH C:501binding site for residue MG C 402
6AC6SOFTWARETYR B:890 , LEU B:910 , ASN B:914 , SER B:916 , GLU B:919 , LYS D:14 , SER D:15 , GLU D:33 , GLY D:35 , SER D:36 , GLY D:37 , LYS D:38 , SER D:39 , SER D:40 , THR D:60 , ILE D:62 , THR D:63 , LYS D:64 , GLN D:134 , ASP D:946 , GLU D:947 , LYS D:994binding site for residue AGS D 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DNY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DNY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DNY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DNY)

(-) Exons   (0, 0)

(no "Exon" information available for 5DNY)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhh..eeee..............hhhhhhh..eee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhh......eeee........................eeee......eeee....eeee.......hhhhhhhhh....eeeeee..........eeeee.....eeee....hhhhhhhhhhhhh.....eeeeeee......hhhhh....eeeeeee...hhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dny A    0 HMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFR  365
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     ||323       333       343       353       363  
                                                                                                                                                                                                                                                                                                                                           305|                                             
                                                                                                                                                                                                                                                                                                                                            320                                             


Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeee...eeeeeee....hhhhhhhhhhhhhh......hhhhhh......eeeeeeeee..eeeeeeeee....eeeeeee..eeee.hhhhhhhhhhhhhh.hhhhhhhhhee...........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeeee..eeee....hhhhhhhhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhh....eeeeee....hhhhh.eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dny B    1 MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGEKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING 1005
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    || 836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996         
                                                                                                                                                                                                                  185|                                                                                                                                                                             
                                                                                                                                                                                                                   832                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhh..eeee..............hhhhhhh..eee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhh......eeee........................eeee......eeee....eeee.......hhhhhhhhhhh..eeeeee..........eeeee.....eeeeee..hhhhhhhhhhhhh.....eeeeeee.hhh..hhhhh.....eeeeee...hhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dny C    1 MMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFR  365
                                    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    || 324       334       344       354       364 
                                                                                                                                                                                                                                                                                                                                          305|                                             
                                                                                                                                                                                                                                                                                                                                           320                                             


Chain D from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee....eeeeee....hhhhhhhhhhhhhh......hhhhhh......eeeeeeeee..eeeeeeeee....eeeeeee..eeee.hhhhhhhhhhhhhh.hhhhhh...ee...........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......eee.....eeeee..eeee....hhhhhhhhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhh.....eeeee.hhhhh....eeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dny D    1 MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING 1005
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997        
                                                                                                                                                                                                                     188|                                                                                                                                                                         
                                                                                                                                                                                                                      836                                                                                                                                                                         


Chain E from PDB  Type:DNA  Length:25
                                                          
                5dny E    1 AAAGTTGGGATTGAGACACACATTC   25
                                    10        20     


Chain F from PDB  Type:DNA  Length:23
                                                        
                5dny F  -26 CGAATGTGTGTCTCAATCCCAAC   -4
                                   -17        -7
   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 5DNY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DNY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DNY)

(-) Gene Ontology  (15, 20)

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
    AGS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dny)
 

(-) 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
  5dny
    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_METJA | Q58719
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RAD50_METJA | Q58718
    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_METJA | Q58719
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RAD50_METJA | Q58718
    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_METJA | Q58719: 3auz 3av0 4tug 4tui 5f3w
        RAD50_METJA | Q58718: 3aux 3auy 3av0 5f3w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DNY)