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(-) Description

Title :  HUMAN APRATAXIN (APTX) BOUND TO RNA-DNA, AMP, AND ZN - PRODUCT COMPLEX
 
Authors :  M. J. Schellenberg, P. S. Tumbale, R. S. Williams
Date :  26 Oct 13  (Deposition) - 18 Dec 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,D,E,G,H
Biol. Unit 1:  A,D,E  (1x)
Biol. Unit 2:  B,G,H  (1x)
Keywords :  Protein-Dna Complex, Dna Repair, 5'-Dna End Processing, Histidine Triad Domain, Hit Domain, Zinc Finger, 5'-Dna End Recognition, Dna Binding Protein-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Tumbale, J. S. Williams, M. J. Schellenberg, T. A. Kunkel, R. S. Williams
Aprataxin Resolves Adenylated Rna-Dna Junctions To Maintain Genome Integrity.
Nature V. 506 111 2013
PubMed-ID: 24362567  |  Reference-DOI: 10.1038/NATURE12824

(-) Compounds

Molecule 1 - APRATAXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APTX, AXA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FORKHEAD-ASSOCIATED DOMAIN HISTIDINE TRIAD-LIKE PROTEIN, FHA-HIT
 
Molecule 2 - 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
    Chains: D, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
    Chains: E, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDEGH
Biological Unit 1 (1x): A DE  
Biological Unit 2 (1x):  B  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3K1Ligand/IonPOTASSIUM ION
4NA1Ligand/IonSODIUM ION
5ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3K-1Ligand/IonPOTASSIUM ION
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3K-1Ligand/IonPOTASSIUM ION
4NA-1Ligand/IonSODIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:171 , SER A:174 , ASP A:193 , LYS A:194 , TYR A:195 , LYS A:197 , HIS A:201 , LEU A:203 , HIS A:251 , PRO A:254 , SER A:255 , MET A:256 , HIS A:260 , HIS A:262 , HOH A:534 , HOH A:574 , HOH A:578 , HOH A:670 , HOH A:674 , G D:1BINDING SITE FOR RESIDUE AMP A 401
2AC2SOFTWARECYS A:319 , CYS A:322 , HIS A:335 , HIS A:339BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWARESER A:255 , HOH A:555 , HOH A:629 , HOH A:681 , HOH D:109 , HOH D:116BINDING SITE FOR RESIDUE NA A 403
4AC4SOFTWARETYR A:195 , CYS A:272 , LYS A:274 , HOH A:518 , GLN B:298 , DT D:3BINDING SITE FOR RESIDUE BME A 404
5AC5SOFTWAREGLY B:170 , LEU B:171 , SER B:174 , ILE B:191 , LYS B:192 , ASP B:193 , LYS B:194 , TYR B:195 , LEU B:203 , HIS B:251 , SER B:255 , MET B:256 , HIS B:260 , HIS B:262 , HOH B:507 , HOH B:527 , HOH B:535 , HOH B:629 , HOH B:630 , HOH B:631 , HOH B:638 , HOH B:673 , G G:1BINDING SITE FOR RESIDUE AMP B 401
6AC6SOFTWARECYS B:319 , CYS B:322 , HIS B:335 , HIS B:339BINDING SITE FOR RESIDUE ZN B 402
7AC7SOFTWARETYR B:195 , CYS B:272 , LYS B:274 , DT G:3 , HOH G:103BINDING SITE FOR RESIDUE BME B 403
8AC8SOFTWAREDT D:8 , DT D:9 , DT E:4 , DC E:5 , HOH E:220 , HOH E:221 , HOH E:236BINDING SITE FOR RESIDUE K E 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NDF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NDF)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh.....eeee...eeeee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhh..............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ndf A 161 GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW 340
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340


Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......ee...eeeee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhh..............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ndf B 161 GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW 340
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340


Chain D from PDB  Type:DNA/RNA  Length:10
                                          
                 4ndf D   1 GTTATGATTC  10
                                    10


Chain E from PDB  Type:DNA  Length:10
                                          
                 4ndf E   1 GAATCATAAC  10
                                    10


Chain G from PDB  Type:DNA/RNA  Length:10
                                          
                 4ndf G   1 GTTATGATTC  10
                                    10


Chain H from PDB  Type:DNA  Length:10
                                          
                 4ndf H   1 GAATCATAAC  10
                                    10
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  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 4NDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4ndf
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  APTX_HUMAN | Q7Z2E3
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 Related Entries

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

UniProtKB/Swiss-Prot
        APTX_HUMAN | Q7Z2E3: 3kt9 4ndg 4ndh 4ndi

(-) Related Entries Specified in the PDB File

3szq 4ndg 4ndh 4ndi