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(-) Description

Title :  STRUCTURE OF CPF1/RNA COMPLEX
 
Authors :  D. Dong, K. Ren, X. Qiu, J. Wang, Z. Huang
Date :  24 Feb 16  (Deposition) - 27 Apr 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dong, K. Ren, X. Qiu, J. Zheng, M. Guo, X. Guan, H. Liu, N. Li, B. Zhang, D. Yang, C. Ma, S. Wang, D. Wu, Y. Ma, S. Fan, J. Wang, N. Gao, Z. Huang
The Crystal Structure Of Cpf1 In Complex With Crispr Rna
Nature V. 532 522 2016
PubMed-ID: 27096363  |  Reference-DOI: 10.1038/NATURE17944

(-) Compounds

Molecule 1 - CPF1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: LACHNOSPIRACEAE BACTERIUM ND2006
    Organism Taxid: 1410628
 
Molecule 2 - RNA (5'- R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)- 3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:716 , A G:19binding site for residue MG A 1301
2AC2SOFTWAREHOH G:201 , HOH G:202 , HOH G:203 , HOH G:204 , HOH G:205 , HOH G:206binding site for residue MG G 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ID6)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:142 -Ser A:143
2Gly A:477 -Lys A:478
3Asn A:607 -Pro A:608
4Gly A:734 -Gln A:735
5Gly A:1109 -Asp A:1110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ID6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ID6)

(-) Exons   (0, 0)

(no "Exon" information available for 5ID6)

(-) 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:1209
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhee.......eehhhhhhhhhhhh...................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.eeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..............hhhhhheeeeee..eeeeeee.hhhhhhhh.........eeeee......hhhhhhhhhhh..hhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhh....eeeeehhhhhhhhhh..eeeeeeehhhhh.......hhhhhhhhhh........eee....eeeee....hhhhh.ee.....ee.........ee.....ee.hhhhhh.eeeeeeeeee........hhhhhhhhhhhh.....eeeeee.....eeeeee.....eeeeee..eeeeee..eeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhhhh................................ee..eeee.......................hhhhhhhhhhhh.eeeee....eeeeeee.hhh.........eeee....eeee.......eeeehhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhh.eee.......eeeeeeee.....eee..............hhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5id6 A    0 AASKLEKFTNCYSLSKTLRFKAIPVGKTQENIDNKRLLVEDEKRAEDYKGVKKLLDRYYLSFINDVLHSIKLKNLNNYISLFRKKTRTEKENKELENLEINLRKEIAKAFKGAAGYKSLFKKDIIETILPEAAKDEIALVNSFNGFTTAFTGFFDNRENmFSEEAKSTSIAFRCINENLTRYISNmDIFEKVDAIFDKHEVQEIKEKILNSDYDVEDFFEGEFFNFVLTQEGIDVYNAIIGGFVTESGEKIKGLNEYINLYNAKTKQALPKFKPLYKQVEGYTSDEEVLEVFRNTLNKNSEIFSSIKKLEKLFKNFDEYSSAGIFVKNGPAISTISKDIFGEWNLIRDKWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKIGSFSLEQLQEYADADLSVVEKLKEIIIQKVDEIYKVYGSSEKLFDADFVLEKSLKKNDAVVAImKDLLDSVKSFENYIKAFFGEGKETNRDESFYGDFVLAYDILLKVDHIYDAIRNYVTQKPYSKDKFKLYFQNPQFmGGWDKDKETDYRATILRYGSKYYLAImDKKYAKCLQKIDKDDVNGNYEKINYKLLPGPNKmLPKVFFSKKWmAYYNPSEDIQKIYKNGTFKKGDmFNLNDCHKLIDFFKDSISRYPKWSNAYDFNFSETEKYKDIAGFYREVEEQGYKVSFESASKKEVDKLVEEGKLYmFQIYNKDFSDKSHGTPNLHTmYFKLLFDENNHGQIRLSGGAELFmRRASLKKEELVVHPANSPIANKNPDNPKKTTTLSYDVYKDKRFSEDQYELHIPIAINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLYIVVVDGKGNIVEQYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNWTSIENIKELKAGYISQVVHKICELVEKYDAVIALEDLNSGFKNSRVKVEKQVYQKFEKmLIDKLNYmVDKKSNPCATGGALKGYQITNKFESFKSmSTQNGFIFYIPAWLTSKIDPSTGFVNLLKTKYTSIADSKKFISSFDRImYVPEEDLFEFALDYKNFSRTDADYIKKWKLYSYGNRIRIFAAAAWEEVCLTSAYKELFNKYGINYQQGDIRALLCEQSDKAFYSSFmALmSLmLQmRNSITGRTDVDFLISPVKNSDGIFYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGQFKKAEDEKLDKVKIAISNKEWLEYAQTSVK 1227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129  ||   141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   |   462       472       482       492       502       512       522       532       542       552     | 562       572       582       592       602|      612       622   |   632       642       652       662       672       682       692       702       712       722       732       742   |   752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942      |952    |  962       972       982   |   992      1002      1012      1022      1032  |   1042      1052      1062      1072     |1088      1098      1108      1118      1128  |  |1138      1148      1158      1168      1178      1188      1198      1208      1218         
                                                                                                                                                              132|                       161-MSE                   187-MSE                                                                                      280|                                                                                                                                                                 456-MSE                                                                    531-MSE                    558-MSE                           592-MSE    603-MSE                626-MSE                                                                    701-MSE              722-MSE                 746-MSE                                                                                                                                                                                                    949-MSE 957-MSE                      986-MSE                                         1035-MSE                                   1078|                                       1128-MSE |  |                                                                                          
                                                                                                                                                               135                                                                                                                                               292                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               1085                                          1131-MSE |                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    1134-MSE                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1137-MSE                                                                                      


Chain G from PDB  Type:RNA  Length:21
                                                      
                5id6 G    3 AAUUUCUACUAAGUGUAGAUC   23
                                    12        22
   Legend:   → Mismatch (orange background)
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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 5ID6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ID6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ID6)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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    Asn A:607 - Pro A:608   [ RasMol ]  
    Gly A:1109 - Asp A:1110   [ RasMol ]  
    Gly A:477 - Lys A:478   [ RasMol ]  
    Gly A:734 - Gln A:735   [ RasMol ]  
 

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