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(-) Description

Title :  CRYSTAL STRUCTURE OF CAS-DNA-N1 COMPLEX
 
Authors :  J. Wang, J. Li, H. Zhao, G. Sheng, M. Wang, M. Yin, Y. Wang
Date :  05 Sep 15  (Deposition) - 11 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Wang, J. Li, H. Zhao, G. Sheng, M. Wang, M. Yin, Y. Wang
Structural And Mechanistic Basis Of Pam-Dependent Spacer Acquisition In Crispr-Cas Systems.
Cell V. 163 840 2015
PubMed-ID: 26478180  |  Reference-DOI: 10.1016/J.CELL.2015.10.008

(-) Compounds

Molecule 1 - CRISPR-ASSOCIATED ENDONUCLEASE CAS1
    ChainsD, C, A, B
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2-281
    GeneYGBT, CAS1, B2755, JW2725
    Organism ScientificESCHERICHIA COLI K12
    Organism Taxid83333
    StrainK12
 
Molecule 2 - 39-MER DNA N1-F
    ChainsG
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 3 - 39-MER DNA N1-R
    ChainsH
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES
 
Molecule 4 - CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2
    ChainsF, E
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-78
    GeneYGBF, CAS2, B2754, JW5438
    Organism ScientificESCHERICHIA COLI K12
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5DLJ)

(-) Sites  (0, 0)

(no "Site" information available for 5DLJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DLJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DLJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DLJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DLJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5DLJ)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeee..eeeeee..eeeeee......eeee...eeeehhhhhhhhhhh.eeeee.hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlj A  15 VSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA 281
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       

Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhheeeeee..eeeeee..eeeee.....eee.hhh.eeeeee...eeeehhhhhhhhhhh.eeeee.hhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlj B   2 TWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA 281
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain C from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhheeeeee..eeeeee..eeeee.....eee.hhh.eeeeee...eeeehhhhhhhhhhh.eeeee.hhh.eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlj C   2 TWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA 281
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

Chain D from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeee..eeeeee..eeeeee......eeee...eeeehhhhhhhhhhh.eeeee.hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlj D  15 VSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA 281
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       

Chain E from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhh..eeee..eeeeeehhhhhhhhhhhhhhhh...eeeeeee......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5dlj E   1 MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRR  78
                                    10        20        30        40        50        60        70        

Chain F from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhh..eeee..eeeeeehhhhhhhhhhhhhhhh...eeeeeee......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 5dlj F   1 MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRR  78
                                    10        20        30        40        50        60        70        

Chain G from PDB  Type:DNA  Length:39
                                                                       
                 5dlj G   1 TTTTTTCGTAGCTGAGGGCCTCAGCTACGTTTTTTTTTT  39
                                    10        20        30         

Chain H from PDB  Type:DNA  Length:39
                                                                       
                 5dlj H   1 TTTTTTCGTAGCTGAGGCCCTCAGCTACGTTTTTTTTTT  39
                                    10        20        30         

   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 5DLJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DLJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DLJ)

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Cis Peptide Bonds" information available for 5dlj)
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAS1_ECOLI | Q468963nkd 3nke 4p6i 4qdl 5dqt 5dqu 5dqz 5ds4 5ds5 5ds6
        CAS2_ECOLI | P459564mak 4p6i 4qdl 5dqt 5dqu 5dqz 5ds4 5ds5 5ds6

(-) Related Entries Specified in the PDB File

5dqt 5dqu 5dqz