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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PENTATRICOPEPTIDE REPEAT PROTEIN PPR10 IN COMPLEX WITH AN 18-NT PSAJ RNA ELEMENT
 
Authors :  P. Yin, Q. Li, C. Yan, Y. Liu, N. Yan
Date :  08 Aug 13  (Deposition) - 30 Oct 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pentatricopeptide Repeats, Superhelical, Rna Binding Protein, Rna, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Yin, Q. Li, C. Yan, Y. Liu, J. Liu, F. Yu, Z. Wang, J. Long, J. He, H. W. Wang, J. Wang, J. K. Zhu, Y. Shi, N. Yan
Structural Basis For The Modular Recognition Of Single-Stranded Rna By Ppr Proteins.
Nature V. 504 168 2013
PubMed-ID: 24162847  |  Reference-DOI: 10.1038/NATURE12651

(-) Compounds

Molecule 1 - CHLOROPLAST PENTATRICOPEPTIDE REPEAT PROTEIN 10
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 69-786
    Gene: PPR10, ZEAMMB73_867042
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: PENTATRICOPEPTIDE REPEAT10
 
Molecule 2 - PSAJ RNA
    Chains: D, C
    Engineered: YES
    Other Details: THIS RNA OLIGO IS SYNTHESIZED BY TAKARA COMPANY.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:441 , ARG B:189 , TYR B:190 , GLU B:191 , ARG B:192BINDING SITE FOR RESIDUE PO4 B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M59)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M59)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M59)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M59)

(-) Exons   (0, 0)

(no "Exon" information available for 4M59)

(-) 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:687
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhh.....hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m59 A  74 PDAQVLVLAISSHPLPTLAAFLASRRDELLRADITSLLKALELSGHWEWALALLRWAGKEGAADASALEMVVRALGREGQHDAVCALLDETPLPPGSRLDVRAYTTVLHALSRAGRYERALELFAELRRQGVAPTLVTYNVVLDVYGRMGRSWPRIVALLDEMRAAGVEPDGFTASTVIAACSRDGLVDEAVAFFEDLKARGHAPSVVTYNALLQVFGKAGNYTEALRVLGEMEQNGCQPDAVTYNELAGTEEAARCLDTMASPNAFTYNTVMTAYGNVGKVDEALALFDQMKKTGFVPNVNTYNLVLGMLGKKSRFTVMLEMLGEMSRSGCTPNRVTWNTMLAVSGKRGMEDYVTRVLEGMRSSGVELSRDTYNTLIAAYGRCGSRTNAFKMYNEMTSAGFTPCITTYNALLNVLSRQGDWSTAQSIVSKMRTKGFKPNEQSYSLLLQCYAKGGNVAGIAAIENEVYGSGAVFPSWVILRTLVIANFKCRRLDGMETAFQEVKARGYNPDLVIFNSMLSIYAKNGMYSKATEVFDSIKRSGLSPDLITYNSLMDMYAKCSESWEAEKILNQLKCSQTMKPDVVSYNTVINGFCKQGLVKEAQRVLSEMVADGMAPCAVTYHTLVGGYSSLEMFSEAREVIGYMVQHGLKPMELTYRRVVESYCRAFEEARGFLSEVKALEAYIEDA 782
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323||     340  ||   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       654       664       674       684       694       704       714       724       734       744     ||756      |775       
                                                                                                                                                                                                                                                                                    324|        343|                                                                                                                                                                                                                                                                                                                                                                                                               750|       763|         
                                                                                                                                                                                                                                                                                     332         348                                                                                                                                                                                                                                                                                                                                                                                                                753        773         


Chain B from PDB  Type:PROTEIN  Length:683
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m59 B  72 LSPDAQVLVLAISSHPLPTLAAFLASRRDELLRADITSLLKALELSGHWEWALALLRWAGKEGAADASALEMVVRALGREGQHDAVCALLDETPLPPGSRLDVRAYTTVLHALSRAGRYERALELFAELRRQGVAPTLVTYNVVLDVYGRMGRSWPRIVALLDEMRAAGVEPDGFTASTVIAACSRDGLVDEAVAFFEDLKARGHAPSVVTYNALLQVFGKAEALRVLGEMEQNGPDAVTYNELAGTYARAGFFEEAARCLDTMAFTYNTVMTAYGNVGKVDEALALFDQMKKTGFVPNVNTYNLVLGMLGKKSRFTVMLEMLGEMSRSGCTPNRVTWNTMLAVSGKRGMEDYVTRVLEGMRSSGVELSRDTYNTLIAAYGRCGSRTNAFKMYNEMTSAGFTPCITTYNALLNVLSRQGDWSTAQSIVSKMRTKGFKPNEQSYSLLLQCYAKGGNVAGIAAIENEVYVFPSWVILRTLVIANFKCRRLDGMETAFQEVKARGYNPDLVIFNSMLSIYAKNGMYSKATEVFDSIKRSGLSPDLITYNSLMDMYAKCSESWEAEKILNQLKCSQTMKPDVVSYNTVINGFCKQGLVKEAQRVLSEMVADGMAPCAVTYHTLVGGYSSLEMFSEAREVIGYMVQHGLKPMELTYRRVVESYCRAKRFEEARGFLKALEAYIEDAQF 784
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 ||    305    || 317       327       337   ||  355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545      |559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759||     781   
                                                                                                                                                                                                                                                       293|         310|                         341|                                                                                                                                                                                                       552|                                                                                                                                                                                                        760|           
                                                                                                                                                                                                                                                        298          313                          350                                                                                                                                                                                                        557                                                                                                                                                                                                         773           


Chain C from PDB  Type:RNA  Length:14
                                              
                 4m59 C   1 GUAUUCAUUAUUUC  18
                                 || 14    
                                 6|       
                                 11       


Chain D from PDB  Type:RNA  Length:18
                                                  
                 4m59 D   1 GUAUUCUUUAAUUAUUUC  18
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4M59)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M59)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M59)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4M59)

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 Related Entries

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        B8Y6I0_MAIZE | B8Y6I0: 4m57 4oe1

(-) Related Entries Specified in the PDB File

4m57