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(-) Description

Title :  X-RAY STRUCTURE OF AAV-2 OBD BOUND TO AAVS1 SITE 3:1
 
Authors :  F. N. Musayev, F. Zarate-Perez, C. R. Escalante
Date :  08 May 15  (Deposition) - 23 Sep 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Dna Binding Protein, Adeno-Associated Virus, Nuclease, Origin-Binding Protein, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. N. Musayev, F. Zarate-Perez, C. Bishop, J. W. Burgner, C. R. Escalante
Structural Insights Into The Assembly Of The Adeno-Associated Virus Type 2 Rep68 Protein On The Integration Site Aavs1.
J. Biol. Chem. V. 290 27487 2015
PubMed-ID: 26370092  |  Reference-DOI: 10.1074/JBC.M115.669960

(-) Compounds

Molecule 1 - PROTEIN REP68
    Chains: A, B, C
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: ORIGIN BINDING DOMAIN (UNP RESIDUES 1-206)
    Gene: REP68
    Mutation: YES
    Organism Common: AAV-2
    Organism Scientific: ADENO-ASSOCIATED VIRUS 2 (ISOLATE SRIVASTAVA/1982)
    Organism Taxid: 648242
    Strain: ISOLATE SRIVASTAVA/1982
 
Molecule 2 - DNA (5'- D(*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*GP*GP*GP*C)- 3')
    Chains: D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*GP*CP*CP*CP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*G)- 3')
    Chains: E
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:83 , HIS A:90 , HIS A:92binding site for residue MN A 301
2AC2SOFTWAREGLU C:83 , HIS C:92 , LYS C:160binding site for residue MN C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZQ9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:23 -Asp A:24
2Gln A:162 -Pro A:163
3Gln B:162 -Pro B:163
4Gln C:162 -Pro C:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZQ9)

(-) 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zq9 A   2 PGFYEIVIKVPSDISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHL 193
                                    11  ||    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
                                       14|                                                                                                                                                                           
                                        22                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zq9 B   2 PGFYEIVIKVPSDLDGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLT 194
                                    11    ||  25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185         
                                         16|                                                                                                                                                                             
                                          21                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zq9 C   2 PGFYEIVIKVPSDSDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHV 196
                                    11  ||    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       
                                       14|                                                                                                                                                                             
                                        23                                                                                                                                                                             


Chain D from PDB  Type:DNA  Length:21
                                                     
                 4zq9 D   1 GCGCTCGCTCGCTCGCTGGGC  21
                                    10        20 


Chain E from PDB  Type:DNA  Length:21
                                                     
                 4zq9 E  22 CGCCCAGCGAGCGAGCGAGCG  42
                                    31        41
   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 4ZQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZQ9)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  REP68_AAV2S | P03132
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  3.6.4.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        REP68_AAV2S | P03132: 1s9h 1u0j 4zo0 5dcx

(-) Related Entries Specified in the PDB File

4zo0