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(-) Description

Title :  STRUCTURE OF MUTANT RIP FROM BARLEY SEEDS IN COMPLEX WITH AMP
 
Authors :  B. -G. Lee, M. K. Kim, S. W. Suh, H. K. Song
Date :  22 May 12  (Deposition) - 31 Oct 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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 :  Hydrolase, Ribosome Inactivating Protein, Rrna N-Glycosylase Activity, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. G. Lee, M. K. Kim, B. W. Kim, S. W. Suh, H. K. Song
Structures Of The Ribosome-Inactivating Protein From Barley Seeds Reveal A Unique Activation Mechanism.
Acta Crystallogr. , Sect. D V. 68 1488 2012
PubMed-ID: 23090398  |  Reference-DOI: 10.1107/S0907444912037110

(-) Compounds

Molecule 1 - PROTEIN SYNTHESIS INHIBITOR I
    Chains: A, B, C, D
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIP30
    Mutation: YES
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: RIBOSOME-INACTIVATING PROTEIN I, RRNA N-GLYCOSIDASE

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:87 , LEU A:88 , GLU A:89 , LEU A:170 , ARG A:178 , HOH A:499 , HOH A:521 , HOH A:590 , HOH A:769BINDING SITE FOR RESIDUE AMP A 301
2AC2SOFTWARETYR B:87 , LEU B:88 , GLU B:89 , LEU B:170 , ARG B:178 , HOH B:481 , HOH B:490 , HOH B:567 , HOH B:810 , HOH B:847 , ARG C:119BINDING SITE FOR RESIDUE AMP B 301
3AC3SOFTWARETYR C:87 , LEU C:88 , GLU C:89 , GLY C:116 , LEU C:170 , ARG C:178 , HOH C:441 , HOH C:603 , HOH C:751 , HOH C:894 , HOH C:918BINDING SITE FOR RESIDUE AMP C 301
4AC4SOFTWAREARG A:119 , TYR D:87 , LEU D:88 , GLY D:116 , THR D:117 , LEU D:170 , ARG D:178 , HOH D:452 , HOH D:500 , HOH D:513 , HOH D:526 , HOH D:546 , HOH D:549 , HOH D:596 , HOH D:721 , HOH D:776BINDING SITE FOR RESIDUE AMP D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FBC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FBC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FBC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FBC)

(-) Exons   (0, 0)

(no "Exon" information available for 4FBC)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh.eehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fbc A   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh.eehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fbc B   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fbc C   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        


Chain D from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhhhhh....ee..ee.............eeeeeee.......eeeeee.....eeeee.....eee.........ee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............hhhhh..hhhhhhhhh............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fbc D   4 KMAKNVDKPLFTATFNVQASSADYATFIAGIRNKLRNPAHFSHNRPVLPPVEPNVPPSRWFHVVLKASPTSAGLTLAIRADNIYLEGFKSSDGTWWELTPGLIPGATYVGFGGTYRDLLGDTDKLTNVALGRQQLADAVTALHGRTKADKPSGPKQQQAREAVTTLLLMVNEATRFQTVSGFVAGLLHPKAVAAASGKIGNEMKAQVNGWQDLSAALLKTDVKPPPGKSPAKFAPIEKMGVRTAVQAANTLGILLFVEVPGGLTVAKALELFHASGGK 281
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
   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 4FBC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FBC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FBC)

(-) Gene Ontology  (7, 7)

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        RIP1_HORVU | P22244: 4fb9 4fba 4fbb 4fbh

(-) Related Entries Specified in the PDB File

4fb9 4fba 4fbb 4fbh