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(-) Description

Title :  CRYSTAL STRUCTURE OF AFC3PO
 
Authors :  E. A. Parizotto, E. D. Lowe, J. S. Parker
Date :  14 Nov 12  (Deposition) - 23 Jan 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.27
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Hydrolase, Translin, Trax, Rna Interference, Rnai, Rna Silencing, Sirna, Passenger Strand, Risc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Parizotto, E. D. Lowe, J. S. Parker
Structural Basis For Duplex Rna Recognition And Cleavage By Archaeoglobus Fulgidus C3Po.
Nat. Struct. Mol. Biol. V. 20 380 2013
PubMed-ID: 23353787  |  Reference-DOI: 10.1038/NSMB.2487

(-) Compounds

Molecule 1 - AFTRAX
    Atcc: 49558
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTWO-E
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: MODIFIED PET-17B
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Other Details: DSMZ, GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES
    Strain: VC-16
    Synonym: AF2260

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:83 , GLU B:118 , HOH B:2001 , HOH B:2002 , HOH B:2003BINDING SITE FOR RESIDUE MG B 197
2AC2SOFTWAREGLU C:83 , GLU C:118BINDING SITE FOR RESIDUE MG C 197
3AC3SOFTWAREGLU D:83 , GLU D:118 , HOH D:2001BINDING SITE FOR RESIDUE MG D 197
4AC4SOFTWAREGLU F:83 , GLU F:118 , HOH F:2001 , HOH F:2002 , HOH F:2003BINDING SITE FOR RESIDUE MG F 197
5AC5SOFTWAREGLU G:83 , GLU G:118 , HOH G:2001BINDING SITE FOR RESIDUE MG G 197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZC1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:102 -Val A:103
2Ala A:187 -Arg A:188
3Glu E:102 -Val E:103
4Ala E:187 -Arg E:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZC1)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZC1)

(-) 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:190
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 A   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 B   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain C from PDB  Type:PROTEIN  Length:189
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARL 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 C   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARL 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain D from PDB  Type:PROTEIN  Length:187
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVA 187
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 D   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVA 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       


Chain E from PDB  Type:PROTEIN  Length:190
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 E   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain F from PDB  Type:PROTEIN  Length:190
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 F   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARLN 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain G from PDB  Type:PROTEIN  Length:189
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARL 189
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 G   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVARL 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain H from PDB  Type:PROTEIN  Length:187
 aligned with O28024_ARCFU | O28024 from UniProtKB/TrEMBL  Length:196

    Alignment length:187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       
         O28024_ARCFU     1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVA 187
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc1 H   1 MRLEECRKRLEELEAAREELLKVLREMRIHSTKSIALIHAGKVEEAEQELKKAIELLEKVKAYREYPEIYFYLCNDAMQELVEAIAFKNAISGEFTFEIDLEVTPAAFLNGFADAVGELRRYALTKLIEGDFKSAERMLEVMEKIYERLMEFTTFPDKLVSGLRKKLDVARGGIERTKSDYIAAKVA 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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  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 3ZC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZC1)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (O28024_ARCFU | O28024)
molecular function
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

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 Related Entries

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

UniProtKB/TrEMBL
        O28024_ARCFU | O28024: 3zc0

(-) Related Entries Specified in the PDB File

3zc0 STRUCTURE OF AFC3PO - DUPLEX RNA COMPLEX