Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  ESCHERICHIA COLI RNASE II
 
Authors :  Y. Zuo, J. Zhang, Y. Wang, A. Malhotra
Date :  13 Sep 06  (Deposition) - 03 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rnase, Exoribonuclease, Ribonuclease, Exonuclease, Nuclease, Hydrolyase, Mrna Decay, Rnr Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zuo, H. A. Vincent, J. Zhang, Y. Wang, M. P. Deutscher, A. Malhotra
Structural Basis For Processivity And Single-Strand Specificity Of Rnase Ii.
Mol. Cell V. 24 149 2006
PubMed-ID: 16996291  |  Reference-DOI: 10.1016/J.MOLCEL.2006.09.004

(-) Compounds

Molecule 1 - EXORIBONUCLEASE 2
    Chains: A, B, C, D
    EC Number: 3.1.13.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RNB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: EXORIBONUCLEASE II, RIBONUCLEASE II, RNASE II

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 60)

Asymmetric Unit (2, 60)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2MSE56Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 14)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:201 , ASP A:209 , ASP A:210BINDING SITE FOR RESIDUE MN A 1001
2AC2SOFTWAREASP B:201 , ASP B:209 , ASP B:210BINDING SITE FOR RESIDUE MN B 1002
3AC3SOFTWAREASP C:201 , ASP C:209 , ASP C:210BINDING SITE FOR RESIDUE MN C 1003
4AC4SOFTWAREASP D:201 , ASP D:209 , ASP D:210BINDING SITE FOR RESIDUE MN D 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ID0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ID0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ID0)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508
 
 
 		  4A:484-508
B:484-508
C:484-508
D:484-508
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508
 
 
 		  1A:484-508
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508
 
 
 		  1-
B:484-508
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508
 
 
 		  1-
-
C:484-508
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_IIPS01175 Ribonuclease II family signature.RNB_ECOLI484-508
 
 
 		  1-
-
-
D:484-508

(-) Exons   (0, 0)

(no "Exon" information available for 2ID0)

(-) Sequences/Alignments

Asymmetric 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:636
 aligned with RNB_ECOLI | P30850 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:640
                                    14        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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644
            RNB_ECOLI     5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
               SCOP domains d2id0a3 A:5-82 Exoribonuclease 2, RNB                                         d2id0a2 A:83-172 Exoribonuclease 2, RNB                                                   d2id0a4 A:173-557 Exoribonuclease 2, RNB                                                                                                                                                                                                                                                                                                                                                         d2id0a1 A:558-644 Exoribonuclease 2, RNB                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeeeee......eeee.....eeeehhhhhh......eeeeeee......eeeeeeeee....eeeeeeeee..eeeeee........ee...............eeeeeeeehhhhh....eeeeeeeee.....hhhhhhhhhhh..............................eee........eeeee.......eeeeeeee.hhhh....hhhhhhhhhhh..eee..eee...hhhhhh.........eeeeeeeeeee...........eeeeeee...eeehhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.....eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhh......eee......................hhhhhhhhhhhhhhh..----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeee.....eeeee.hhh..hhh.eeee....eeee..eeeee...eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_II          ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2id0 A   5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQmKKVmHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEmRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEmLDEGLVREDLTALDFVTIDSASTEDmDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPmLPRELSDDLCSLRANEVRPVLACRmTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAmIAANICAARVLRDKLGFGIYNVHmGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDmINHRLLKAVIKG----RPQDEITVQmAERRRLNRmAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGmRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRmETRSIIARPVA 644
                                    14        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       284 |     294       304       314       324       334       344       354       364       374       384       394       404       414  |    424       434       444       454       464       474       484       494       504|      514  |    524      |534     | 544       554       564       574 |     584       594       604       614       624       634       644
                                                                         51-MSE                                                                          132-MSE                                           182-MSE                   208-MSE                                              261-MSE                  286-MSE                                                                                                    393-MSE                 417-MSE                                                                                 505-MSE     517  522      531-MSE  540-MSE                             576-MSE                                                  633-MSE       
                                                                             55-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:636
 aligned with RNB_ECOLI | P30850 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:640
                                    14        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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644
            RNB_ECOLI     5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
               SCOP domains d2id0b3 B:5-82 Exoribonuclease 2, RNB                                         d2id0b2 B:83-172 Exoribonuclease 2, RNB                                                   d2id0b4 B:173-557 Exoribonuclease 2, RNB                                                                                                                                                                                                                                                                                                                                                         d2id0b1 B:558-644 Exoribonuclease 2, RNB                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......eeeeeee......eeee.....eeeehhhhhh......eeeeeeee....eeeeeeeeee....eeeeeeeee..eeeeee........eeeee............eeeeeeeehhhhh....eeeeeeeee.....hhhhhhhhhhhh....................ee.......eee........eeeeeeee...eeeeeeeee.hhhh....hhhhhhhhhhh..eee..eee...hhhhhh.........eeeeeeeeeee..........eeeeeeee...eeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eee......................hhhhhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeee.....eeeee.hhh..hhh.eeee....eeee..eeeee...eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_II          ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2id0 B   5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQmKKVmHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEmRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEmLDEGLVREDLTALDFVTIDSASTEDmDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPmLPRELSDDLCSLRANEVRPVLACRmTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAmIAANICAARVLRDKLGFGIYNVHmGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDmINHRLLKAVIKG----RPQDEITVQmAERRRLNRmAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGmRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRmETRSIIARPVA 644
                                    14        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       284 |     294       304       314       324       334       344       354       364       374       384       394       404       414  |    424       434       444       454       464       474       484       494       504|      514  |    524      |534     | 544       554       564       574 |     584       594       604       614       624       634       644
                                                                         51-MSE                                                                          132-MSE                                           182-MSE                   208-MSE                                              261-MSE                  286-MSE                                                                                                    393-MSE                 417-MSE                                                                                 505-MSE     517  522      531-MSE  540-MSE                             576-MSE                                                  633-MSE       
                                                                             55-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:636
 aligned with RNB_ECOLI | P30850 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:640
                                    14        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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644
            RNB_ECOLI     5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
               SCOP domains d2id0c3 C:5-82 Exoribonuclease 2, RNB                                         d2id0c2 C:83-172 Exoribonuclease 2, RNB                                                   d2id0c4 C:173-557 Exoribonuclease 2, RNB                                                                                                                                                                                                                                                                                                                                                         d2id0c1 C:558-644 Exoribonuclease 2, RNB                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeeeee......eeeeee..eeeee..hhhhh.....eeeeeee......eeeeeeeee....eeeeeeeee..eeeeee........eeeee............eeeeeeeehhhhh....eeeeeeeee.....hhhhhhhhhhh.....................ee......eeee........eeeeeeee...eeeeeeeee.hhhh....hhhhhhhhhhh..eee..eee...hhhhhhh.........eeeeeeeeee..........eeeeeee...eeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...eee......................hhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeee.....eeeee.hhh..hhh.eeee....eeee..eeeee...eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_II          ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2id0 C   5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQmKKVmHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEmRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEmLDEGLVREDLTALDFVTIDSASTEDmDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPmLPRELSDDLCSLRANEVRPVLACRmTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAmIAANICAARVLRDKLGFGIYNVHmGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDmINHRLLKAVIKG----RPQDEITVQmAERRRLNRmAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGmRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRmETRSIIARPVA 644
                                    14        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       284 |     294       304       314       324       334       344       354       364       374       384       394       404       414  |    424       434       444       454       464       474       484       494       504|      514  |    524      |534     | 544       554       564       574 |     584       594       604       614       624       634       644
                                                                         51-MSE                                                                          132-MSE                                           182-MSE                   208-MSE                                              261-MSE                  286-MSE                                                                                                    393-MSE                 417-MSE                                                                                 505-MSE     517  522      531-MSE  540-MSE                             576-MSE                                                  633-MSE       
                                                                             55-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:636
 aligned with RNB_ECOLI | P30850 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:640
                                    14        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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644
            RNB_ECOLI     5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQDEITVQMAERRRLNRMAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIARPVA 644
               SCOP domains d2id0d3 D:5-82 Exoribonuclease 2, RNB                                         d2id0d2 D:83-172 Exoribonuclease 2, RNB                                                   d2id0d4 D:173-557 Exoribonuclease 2, RNB                                                                                                                                                                                                                                                                                                                                                         d2id0d1 D:558-644 Exoribonuclease 2, RNB                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....eeee............eeeeeee......eeeeeeeee....eeeeeeee....eeeee........eeeee............eeeeeeeehhhhhh...eeeeeeeee.....hhhhhhhhhhh.....................eeeeeeeeeeee........eeeeeee.....eeeeeeee.........hhhhhhhhhhh..eee..eee...hhhhhhh........eeeeeeeeeee.....eeeeeeeeeeeeeeeeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhh...eee......................hhhhhhhhhhhhhhhh.----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..eeeeee.....eeeee.hhh..hhh.eeee....eeee..eeeee...eeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBONUCLEASE_II          ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2id0 D   5 NPLLAQLKQQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQmKKVmHGDRIIAVIHSEKERESAEPEELVEPFLTRFVGKVQGKNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEmRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAPDGVATEmLDEGLVREDLTALDFVTIDSASTEDmDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPmLPRELSDDLCSLRANEVRPVLACRmTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAmIAANICAARVLRDKLGFGIYNVHmGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDmINHRLLKAVIKG----RPQDEITVQmAERRRLNRmAERDVGDWLYARFLKDKAGTDTRFAAEIVDISRGGmRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRmETRSIIARPVA 644
                                    14        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       284 |     294       304       314       324       334       344       354       364       374       384       394       404       414  |    424       434       444       454       464       474       484       494       504|      514  |    524      |534     | 544       554       564       574 |     584       594       604       614       624       634       644
                                                                         51-MSE                                                                          132-MSE                                           182-MSE                   208-MSE                                              261-MSE                  286-MSE                                                                                                    393-MSE                 417-MSE                                                                                 505-MSE     517  522      531-MSE  540-MSE                             576-MSE                                                  633-MSE       
                                                                             55-MSE
   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  (2, 16)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Fold: OB-fold (1179)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ID0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ID0)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RNB_ECOLI | P30850)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0008859    exoribonuclease II activity    Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0016070    RNA metabolic process    The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000178    exosome (RNase complex)    A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2id0)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2id0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RNB_ECOLI | P30850
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.13.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RNB_ECOLI | P30850
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RNB_ECOLI | P30850: 2ix0 2ix1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ID0)