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(-) Description

Title :  HUMAN APRATAXIN (APTX) BOUND TO RNA-DNA AND ZN - ADENOSINE VANADATE TRANSITION STATE MIMIC 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 :  2.54
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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1V5A2Ligand/IonADENOSINE-5'-VANADATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1V5A1Ligand/IonADENOSINE-5'-VANADATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1V5A1Ligand/IonADENOSINE-5'-VANADATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:171 , SER A:174 , ASP A:193 , LYS A:194 , TYR A:195 , LYS A:197 , LEU A:203 , HIS A:251 , SER A:255 , MET A:256 , HIS A:260 , HIS A:262 , HOH A:501 , G D:1BINDING SITE FOR RESIDUE V5A A 401
2AC2SOFTWARECYS A:319 , CYS A:322 , HIS A:335 , HIS A:339BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWARELEU B:171 , SER B:174 , ILE B:191 , LYS B:192 , ASP B:193 , LYS B:194 , LYS B:197 , LEU B:203 , HIS B:251 , SER B:255 , MET B:256 , HIS B:260 , HIS B:262 , G G:1BINDING SITE FOR RESIDUE V5A B 401
4AC4SOFTWARECYS B:319 , CYS B:322 , HIS B:335 , HIS B:339BINDING SITE FOR RESIDUE ZN B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NDG)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeee...eeeee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhh..............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndg A 164 MGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHWT 341
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333        


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee...eeeee........eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.........eeeee.........hhhhhhhhhh..eeehhhhhhhhhhhh......hhhhhhh.............hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndg B 164 MGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHW 340
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       


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


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


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


Chain H from PDB  Type:DNA  Length:10
                                          
                 4ndg H   1 GAATCATAAC  10
                                    10
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  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 4NDG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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  4ndg
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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 4ndf 4ndh 4ndi

(-) Related Entries Specified in the PDB File

3szq 4ndf 4ndh 4ndi