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(-) Description

Title :  CRYSTAL STRUCTURE OF MJMRE11-DNA2 COMPLEX
 
Authors :  S. Sung, Y. Cho
Date :  24 Jun 14  (Deposition) - 15 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.55
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Nuclease, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sung, F. Li, Y. B. Park, J. S. Kim, A. K. Kim, O. K. Song, J. Kim, J. Che, S. E. Lee, Y. Cho
Dna End Recognition By The Mre11 Nuclease Dimer: Insights Into Resection And Repair Of Damaged Dna.
Embo J. V. 33 2422 2014
PubMed-ID: 25107472  |  Reference-DOI: 10.15252/EMBJ.201488299

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    Chains: C, A, B, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-333
    Gene: MRE11, MJ1323
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
 
Molecule 2 - DNA (5'-D(P*GP*CP*AP*CP*GP*TP*AP*GP*GP*AP*CP*AP*GP*C)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*TP*GP*TP*CP*CP*TP*AP*CP*GP*TP*GP*CP*CP*A)- 3')
    Chains: H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MG12Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP C:49 , ASN C:84 , HIS C:158 , HIS C:186 , MG C:402binding site for residue MG C 401
02AC2SOFTWAREASP C:8 , HIS C:10 , ASP C:49 , HIS C:188 , MG C:401binding site for residue MG C 402
03AC3SOFTWAREASP A:49 , ASN A:84 , HIS A:158 , HIS A:186 , MG A:402binding site for residue MG A 401
04AC4SOFTWAREASP A:8 , HIS A:10 , ASP A:49 , HIS A:188 , MG A:401binding site for residue MG A 402
05AC5SOFTWAREASP B:49 , ASN B:84 , HIS B:158 , HIS B:186 , MG B:402binding site for residue MG B 401
06AC6SOFTWAREASP B:8 , HIS B:10 , ASP B:49 , HIS B:188 , MG B:401binding site for residue MG B 402
07AC7SOFTWAREASP D:49 , ASN D:84 , HIS D:158 , HIS D:186 , MG D:402 , HOH D:501binding site for residue MG D 401
08AC8SOFTWAREASP D:8 , HIS D:10 , ASP D:49 , HIS D:188 , MG D:401 , HOH D:501binding site for residue MG D 402
09AC9SOFTWAREASP E:49 , ASN E:84 , HIS E:158 , HIS E:186 , MG E:402binding site for residue MG E 401
10AD1SOFTWAREASP E:8 , HIS E:10 , ASP E:49 , HIS E:188 , MG E:401 , HOH E:503binding site for residue MG E 402
11AD2SOFTWAREASP F:49 , ASN F:84 , HIS F:158 , HIS F:186 , MG F:402binding site for residue MG F 401
12AD3SOFTWAREASP F:8 , HIS F:10 , ASP F:49 , HIS F:186 , HIS F:188 , MG F:401 , HOH F:501binding site for residue MG F 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1Asn C:116 -Gly C:117
2Leu C:167 -Asp C:168
3Gly A:-2 -Ser A:-1
4Asn A:116 -Gly A:117
5Leu A:167 -Asp A:168
6Asn B:116 -Gly B:117
7Leu B:167 -Asp B:168
8Asn D:116 -Gly D:117
9Leu D:167 -Asp D:168
10Gly E:-2 -Ser E:-1
11Asn E:116 -Gly E:117
12Leu E:167 -Asp E:168
13Asn F:116 -Gly F:117
14Leu F:167 -Asp F:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TUG)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh...eeee..............hhhhhhh...ee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeeee.............hhhhh....eeeee.....eeeee..eeeee..........hhhhhhhhh.eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh.eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tug A  -3 RGSHMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPDN 313
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhh..eeee..hhhhh.......hhhhhhh...ee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee.............hhhhh....eeeee.....eeee....eeee.......hhhhhhhhhhh..eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tug B   1 MMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDE 306
                                    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      


Chain C from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh...eeee..hhhhh.......hhhhhhh...ee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhh.....eeeee..............hhhhh....eeee......eeeee..eeeee..........hhhhhhhh..eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh.eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tug C   0 HMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPD 312
                                     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       309   


Chain D from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh...eeee..hhhhh.......hhhhhhh..eee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee.............hhhhh....eeeee.....eeeee..eeeee.......hhhhhhhhhhh..eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.ee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tug D   0 HMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDE 306
                                     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       


Chain E from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh...eeee..............hhhhhhh..eee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh....eeeee..............hhhhh....eeee......eeee....eeee..........hhhhhhhh..eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhh.eeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tug E  -2 GSHMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMP 311
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    


Chain F from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh...eeee..............hhhhhhh...ee..eeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhh....eeeee..............hhhhh....eeee......eeeee..eeeee..........hhhhhhhh..eeeee.......hhh.eeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhh.ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tug F  -1 SHMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIV 303
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     


Chain G from PDB  Type:DNA  Length:14
                                              
                 4tug G   1 GCACGTAGGACAGC  14
                                    10    


Chain H from PDB  Type:DNA  Length:15
                                               
                 4tug H  15 CTGTCCTACGTGCCA  29
                                    24
   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 4TUG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:116 - Gly A:117   [ RasMol ]  
    Asn B:116 - Gly B:117   [ RasMol ]  
    Asn C:116 - Gly C:117   [ RasMol ]  
    Asn D:116 - Gly D:117   [ RasMol ]  
    Asn E:116 - Gly E:117   [ RasMol ]  
    Asn F:116 - Gly F:117   [ RasMol ]  
    Gly A:-2 - Ser A:-1   [ RasMol ]  
    Gly E:-2 - Ser E:-1   [ RasMol ]  
    Leu A:167 - Asp A:168   [ RasMol ]  
    Leu B:167 - Asp B:168   [ RasMol ]  
    Leu C:167 - Asp C:168   [ RasMol ]  
    Leu D:167 - Asp D:168   [ RasMol ]  
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    Leu F:167 - Asp F:168   [ RasMol ]  
 

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  4tug
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  MRE11_METJA | Q58719
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 Related Entries

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

UniProtKB/Swiss-Prot
        MRE11_METJA | Q58719: 3auz 3av0 4tui 5dny 5f3w

(-) Related Entries Specified in the PDB File

4tui