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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII
 
Authors :  A. G. Gabdulkhakov, I. V. Mitroshin, M. B. Garber
Date :  20 Aug 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Ribosome, P-Stalk, Archaea, Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. G. Gabdulkhakov, I. V. Mitroshin, M. B. Garber
Crystal Structure Of The Base Of The Ribosomal P Stalk From Methanococcus Jannaschii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 74 NT FRAGMENT OF 23S RRNA
    ChainsA, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMJA23S-74.UC18
    Expression System StrainXL1(BLUE)
    Expression System Taxid469008
    Expression System Vector TypePUC18
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L10
    ChainsB, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-11C/MJAP0NTF
    Expression System Taxid469008
    Expression System VariantPUBS520
    Expression System VectorPET-11C
    Expression System Vector TypePLASMID
    GeneRPL10, RPLP0, MJ0509
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190
    SynonymACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG,MJAL10
 
Molecule 3 - 50S RIBOSOMAL PROTEIN L11
    ChainsC, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-11C/MJAL11
    Expression System Taxid469008
    Expression System VariantPUBS520
    Expression System Vector TypePET-11C
    GeneRPL11, MJ0373
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2K5Ligand/IonPOTASSIUM ION
3MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA A:1179 , A A:1180 , C A:1182 , A A:1183binding site for residue MG A 1301
02AC2SOFTWAREG A:1166 , U A:1211binding site for residue MG A 1302
03AC3SOFTWAREA A:1183 , U A:1204binding site for residue MG A 1303
04AC4SOFTWAREG A:1166 , A A:1167 , A A:1196 , G A:1197 , G A:1199binding site for residue MG A 1304
05AC5SOFTWAREU A:1191 , U A:1192 , U A:1193 , A A:1196 , HOH A:1402 , HOH A:1405binding site for residue MG A 1305
06AC6SOFTWAREG A:1164 , G A:1165 , A A:1194binding site for residue CL A 1306
07AC7SOFTWAREU A:1171 , G A:1172 , G A:1173 , A A:1180binding site for residue K A 1307
08AC8SOFTWAREC A:1216 , MET B:58 , SER B:59 , ASN B:61 , ARG B:89 , ALA B:91binding site for residue K A 1308
09AC9SOFTWARELYS B:79 , ILE B:204binding site for residue CL B 301
10AD1SOFTWARELYS C:110 , MET C:113 , SER C:115binding site for residue K C 201
11AD2SOFTWAREA D:1183 , U D:1204binding site for residue MG D 1301
12AD3SOFTWAREA D:1180 , C D:1182binding site for residue MG D 1302
13AD4SOFTWAREHOH D:1401 , HOH D:1402 , HOH D:1404 , HOH D:1405 , HOH D:1406 , HOH D:1407binding site for residue MG D 1303
14AD5SOFTWAREA D:1179 , A D:1180 , C D:1182 , A D:1183binding site for residue K D 1304
15AD6SOFTWAREMET F:108 , LYS F:109 , ALA F:112binding site for residue CL F 201
16AD7SOFTWAREASP E:48 , MET F:113 , LEU F:114 , SER F:115binding site for residue K F 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly C:17 -Pro C:18
2Gly F:17 -Pro F:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DAR)

(-) 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:RNA  Length:74
                                                                                                           
                5dar A 1151 GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGCUCACCCGUCGAGGC 1224
                                  1160      1170      1180      1190      1200      1210      1220    

Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhheeee...............hhhhhhhhhhhh...eeee.eeeeee....eehhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dar B    9 MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKV  212
                                    18        28        38        48        58        68        78        88        98       108       118     ||172       182       192       202       212
                                                                                                                                             124|                                           
                                                                                                                                              169                                           

Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.........hhhhhh....hhhhhhhhhhhhh......eeeeeeeee....eeeeee...hhhhhhhhhhh.............eeehhhhhhhhhhhhh......hhhhhhhhhhhhhh...eee...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dar C    1 AKEVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVDTETRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSYTLKNAVKEVLGTCGSMGVTVEGKDPKEVQKEIDAGVYDEYFK  158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain D from PDB  Type:RNA  Length:74
                                                                                                           
                5dar D 1151 GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGCUCACCCGUCGAGGC 1224
                                  1160      1170      1180      1190      1200      1210      1220    

Chain E from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...........hhhhh...eeeeee..hhhhhhhhhhhheeee.....ee.........ee......hhhhhhhhh...eeee..eeee...........eehhhhhhhhhhhh...eeee.eeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dar E    9 MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVD  213
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     

Chain F from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee........hhhhhhhhhh.hhhhhhhhhhhhh......eeeeeeeee.....eeeee...hhhhhhhhhhh..............eehhhhhhhhhhhh.......hhhhhhhhhhhhhh....ee...hhhhhhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dar F    1 AKEVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVDTETRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSYTLKNAVKEVLGTCGSMGVTVEGKDPKEVQKEIDAGVYDEYFK  158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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 5DAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 20)

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 Related Entries

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

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        RL10_METJA | P540493jsy 5d6g 5d8h
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(-) Related Entries Specified in the PDB File

5col RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII
5d6g CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII
5d8h CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON