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(-) Description

Title :  CRYSTAL STRUCTURE OF ACIDAMINOCOCCUS SP. CPF1 IN COMPLEX WITH CRRNA AND TARGET DNA
 
Authors :  T. Yamano, H. Nishimasu, H. Hirano, T. Nakane, R. Ishitani, O. Nureki
Date :  30 Mar 16  (Deposition) - 04 May 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nuclease, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yamano, H. Nishimasu, B. Zetsche, H. Hirano, I. M. Slaymaker, Y. Li, I. Fedorova, T. Nakane, K. S. Makarova, E. V. Koonin, R. Ishitani, F. Zhang, O. Nureki
Crystal Structure Of Cpf1 In Complex With Guide Rna And Target Dna
Cell V. 165 949 2016
PubMed-ID: 27114038  |  Reference-DOI: 10.1016/J.CELL.2016.04.003

(-) Compounds

Molecule 1 - CRISPR-ASSOCIATED ENDONUCLEASE CPF1
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CPF1
    Organism Scientific: ACIDAMINOCOCCUS SP. BV3L6
    Organism Taxid: 1111120
    Strain: BV3L6
    Synonym: ASCPF1
 
Molecule 2 - RNA (43-MER)
    Chains: B
    Engineered: YES
    Organism Scientific: ACIDAMINOCOCCUS
    Organism Taxid: 904
    Synonym: CRRNA
    Synthetic: YES
 
Molecule 3 - DNA (34-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: ACIDAMINOCOCCUS
    Organism Taxid: 904
    Synonym: TARGET DNA
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: ACIDAMINOCOCCUS
    Organism Taxid: 904
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:12 , TYR A:597 , ASN A:715 , TYR A:879binding site for residue EDO A 1401
2AC2SOFTWARETHR A:2 , GLN A:3 , GLY A:6 , PHE A:7 , ARG A:891binding site for residue EDO A 1402
3AC3SOFTWAREPHE A:1079 , VAL A:1080 , MET A:1119 , LEU A:1129 , PRO A:1130 , GLY A:1131 , GLN A:1303binding site for residue EDO A 1403
4AC4SOFTWARELYS A:757 , A B:-4binding site for residue NA A 1404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B43)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B43)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B43)

(-) Exons   (0, 0)

(no "Exon" information available for 5B43)

(-) 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:1272
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.....eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh.hhhhhhhhhhhhhh...........hhhhhhhhhhhh.hhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eehhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee............hhhhhhhhheeeeee..eeeeee.......................eeeeeee..hhhhhhhhhh..hhhhhhhhhhh...eee.......eeehhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh............hhhhh.hhhhhhhhhh...eeeeeee.hhhhhhhhhhh...eeeeeehhhhh.......hhhhhhhhhhhhhhhhhh...ee....eeeee......eee...........hhhhhhhhhhhhh.......hhhhhhh.....eee........hhhhh.eeeeeeeeee.........hhhhhhhhhhhhh....eeeee.......eeeee.....eeeeee..ee..eehhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh................................ee..eeee........................hhhhhhhhhhheeeeee......eeeeee...hhhhh........eeeeee....eee.....eee...eee..eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeee............hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5b43 A    1 MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKTYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDNLTDAINKRHAEIYKGLFKAELFNGKVLKQLTTTEHENALLRSFDKFTTYFSGFYENRKNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVSTSIEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAHIIASLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFNELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLKHEDINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDSLLGLYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEKFKLNFQMPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKTSEGFDKMYYDYFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDLNNPEKEPKKFQTAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSSQYKDLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNLHTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSRMEKMLNKKLKDQKTPIPDTLYQELYDYVNHRLSHDLSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPITLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTIQQFDYQKKLDNREKERVAARQAWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVVLENLAVYQQFEKMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQFTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFVDPFVWKTIKNHESRKHFLEGFDFLHYDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVPYRDLYPANELIALLEEKGIVFRDGSNILPKLLENDDSHAIDTMVALIRSVLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPMDADANGAYHIALKGQLLLNHLKESKDLKLQNGISNQDWLAYIQELRN 1307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793 ||    811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991   || 1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305  
                                                                                                                                                                           146|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  795|                                                                                                                                                                                            995|                                                                                                                                                    1162|                                                                                                                                      
                                                                                                                                                                            150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   804                                                                                                                                                                                            1010                                                                                                                                                     1173                                                                                                                                      


Chain B from PDB  Type:RNA  Length:40
                                                                         
                5b43 B  -19 AAUUUCUACUCUUGUAGAUGGAAAUUAGGUGCGCUUGGCA   20
                                   -10         0        10        20


Chain C from PDB  Type:DNA  Length:30
                                                               
                5b43 C  -19 GCCAAGCGCACCTAATTTCCTAAAGGACTG   10
                                   -10         0        10


Chain D from PDB  Type:DNA  Length:10
                                           
                5b43 D  -10 CAGTCCTTTA   -1
                                    -1
   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 5B43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B43)

(-) Gene Ontology  (5, 5)

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  5b43
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        CPF1_ACISB | U2UMQ6: 5kk5 5xh6 5xh7

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