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(-) Description

Title :  THE CATALYTIC CORE OF RAD2 IN COMPLEX WITH DNA SUBSTRATE (COMPLEX III)
 
Authors :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, M. Nowotny
Date :  02 Apr 14  (Deposition) - 27 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Ba Rossmann-Like, Dna Repair, Tfiih, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mietus, E. Nowak, M. Jaciuk, P. Kustosz, J. Studnicka, M. Nowotny
Crystal Structure Of The Catalytic Core Of Rad2: Insights Into The Mechanism Of Substrate Binding.
Nucleic Acids Res. V. 42 10762 2014
PubMed-ID: 25120270  |  Reference-DOI: 10.1093/NAR/GKU729

(-) Compounds

Molecule 1 - RAD2P
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) ROSSETA
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Fragment: RAD2 CATALYTIC CORE
    Gene: RAD2, YGR258C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - DNA (5'- D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
    Chains: D, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2K4Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:794 , ASP A:813 , ASP A:815 , HOH A:1117 , HOH A:1178BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWARELEU A:869 , MET A:872 , HOH A:1126 , HOH A:1285 , DG C:9 , DA D:9 , HOH D:116BINDING SITE FOR RESIDUE K A 1002
3AC3SOFTWARELYS B:84 , GLU B:794 , ASP B:813 , ASP B:815 , ASP B:864 , HOH B:1183 , HOH B:1224BINDING SITE FOR RESIDUE CA B 1001
4AC4SOFTWARELEU B:860 , LEU B:861 , LEU B:869 , MET B:872 , HOH B:1135 , HOH B:1230 , DG C:9 , HOH C:102 , DA D:9BINDING SITE FOR RESIDUE K B 1002
5AC5SOFTWAREGLU E:794 , ASP E:813 , ASP E:815 , ASP E:864 , HOH E:1149BINDING SITE FOR RESIDUE CA E 1001
6AC6SOFTWARELEU E:869 , MET E:872 , HOH E:1109 , HOH E:1111 , HOH E:1132 , DG G:9 , DA H:9BINDING SITE FOR RESIDUE K E 1002
7AC7SOFTWAREGLU F:794 , ASP F:813 , ASP F:815 , ASP F:864 , HOH F:1101 , HOH F:1258BINDING SITE FOR RESIDUE CA F 1001
8AC8SOFTWARELEU F:869 , MET F:872 , HOH F:1114 , HOH F:1248 , DG G:9 , DA H:9 , HOH H:108BINDING SITE FOR RESIDUE K F 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q0Z)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:929 -Pro A:930
2Phe B:929 -Pro B:930
3Phe E:929 -Pro E:930
4Phe F:929 -Pro F:930

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q0Z)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeee.hhhh..eeeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh....eee.......eeeeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0z A   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDQEGNAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKERRQGKRESAKSDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41        51        61        71        81        91       101  ||   771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981  
                                                                                                                                104|                                                                                                                                                                                                                          
                                                                                                                                 765                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeee.hhhh..eeeee..hhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh....eee...hhhhhh....eee.......eeeeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0z B   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDQNAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQSDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41   ||   53        63        73        83      |766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       
                                                                      45|                                        90|                                                                                                                                                                                                                           
                                                                       48                                        764                                                                                                                                                                                                                           


Chain C from PDB  Type:DNA  Length:17
                                                 
                 4q0z C   0 TGCTCCCTTGTCTCAGT  16
                                     9       


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4q0z D   0 TCTGAGACAAGGGAGCT  16
                                     9       


Chain E from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhee.hhhhhh..eeeee..hhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh....eee.........eeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0z E   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRDQEAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKQETENKFEKDLRKKLVNNEIILDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41    ||  53        63        73        83       765       775       785       795       805       815       825       835       845       855       865       875       885       895    || 907       917       929       939       949       959       969       979    
                                                                       46|                                         92|                                                                                                                                    900|                   925|                                                       
                                                                        49                                         765                                                                                                                                     903                    928                                                       


Chain F from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...hhhhhh..eeeee..hhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhh....eee...hhhhhh....eee.........eeehhhhhhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0z F   2 GVHSFWDIAGPTARPVRLESLEDKRMAVDASIWIYQFLKAVRAVKNSHITGFFRRICKLLYFGIRPVFVFDGGVPVLKRETIRQRKERDEVTMDMIKEVQELLSRFGIPYITAPMEAEAQCAELLQLNLVDGIITDDSDVFLFGGTKIYKNMFHEKNYVEFYDAESILKLLGLDRKNMIELAQLLGSDYTNGLKGMGPVSSIEVIAEFGNLKNFKDWYNNGQFDKRKQETENKFEKDLRKKLVNNEIILDDDFPSVMVYDAYMRPEVDHDTTPFVWGVPDLDMLRSFMKTQLGWPHEKSDEILIPLI 983
                                    11        21        31        41 ||     56        66        76        86       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       
                                                                    43|                                           94|                                                                                                                                                                                                                          
                                                                     49                                           765                                                                                                                                                                                                                          


Chain G from PDB  Type:DNA  Length:17
                                                 
                 4q0z G   0 TGCTCCCTTGTCTCAGT  16
                                     9       


Chain H from PDB  Type:DNA  Length:17
                                                 
                 4q0z H   0 TCTGAGACAAGGGAGCT  16
                                     9
   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 4Q0Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q0Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q0Z)

(-) Gene Ontology  (17, 17)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD2_YEAST | P07276: 2lox 4q0r 4q0w 4q10

(-) Related Entries Specified in the PDB File

4q0r 4q0w 4q10