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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
 
Authors :  A. G. Gabdulkhakov, I. V. Mitroshin, M. B. Garber
Date :  17 Aug 15  (Deposition) - 24 Aug 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribosome, P-Stalk, Archaea, Antibiotic, Thiostrepton, 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 With Antibiotic Thiostrepton
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 23S RIBOSOMAL RNA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMJA23S-74.UC18
    Expression System Strain: XL1(BLUE)
    Expression System Taxid: 469008
    Expression System Vector Type: PUC18
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
 
Molecule 2 - 50S RIBOSOMAL PROTEIN L10
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11C/MJAP0NTF
    Expression System Taxid: 469008
    Expression System Variant: PUBS520
    Expression System Vector: PET-11C
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 9-221
    Gene: RPL10, RPLP0, MJ0509
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG,MJAL10
 
Molecule 3 - 50S RIBOSOMAL PROTEIN L11
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11C/MJAL11
    Expression System Taxid: 469008
    Expression System Variant: PUBS520
    Expression System Vector Type: PET-11C
    Gene: RPL11, MJ0373
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
 
Molecule 4 - THIOSTREPTON
    Chains: D
    Organism Scientific: STREPTOMYCES AZUREUS
    Organism Taxid: 146537

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 42)

Asymmetric/Biological Unit (12, 42)
No.NameCountTypeFull Name
1BB94Mod. Amino Acid(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2DBU1Mod. Amino Acid(2Z)-2-AMINOBUT-2-ENOIC ACID
3DCY1Mod. Amino AcidD-CYSTEINE
4DHA3Mod. Amino Acid2-AMINO-ACRYLIC ACID
5MG11Ligand/IonMAGNESIUM ION
6MH61Mod. Amino Acid3-HYDROXY-2-IMINOPROPANOIC ACID
7MSE11Mod. Amino AcidSELENOMETHIONINE
8NA4Ligand/IonSODIUM ION
9NH21Mod. Amino AcidAMINO GROUP
10QUA1Mod. Amino Acid8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
11TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
12TS91Mod. Amino Acid(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:1166 , HOH A:1405 , HOH A:1414 , HOH A:1417 , HOH A:1429 , HOH A:1434binding site for residue MG A 1301
02AC2SOFTWAREA A:1183 , G A:1203 , U A:1204 , HOH A:1409 , HOH A:1416 , HOH A:1422 , HOH A:1428binding site for residue MG A 1302
03AC3SOFTWAREG A:1173 , A A:1180 , C A:1182 , G A:1184 , NA A:1313 , HOH A:1432 , HOH A:1437binding site for residue MG A 1303
04AC4SOFTWAREHOH A:1403 , HOH A:1420 , HOH A:1431 , HOH A:1440 , HOH A:1442 , HOH A:1454binding site for residue MG A 1304
05AC5SOFTWAREHOH A:1413 , HOH A:1424 , HOH A:1425 , HOH A:1439 , HOH A:1448 , HOH A:1451binding site for residue MG A 1305
06AC6SOFTWAREHOH A:1412 , HOH A:1436 , HOH A:1445 , HOH A:1446 , HOH A:1449 , HOH A:1453binding site for residue MG A 1306
07AC7SOFTWAREG A:1181 , A A:1208 , HOH A:1408 , HOH A:1427 , HOH A:1435 , HOH A:1457binding site for residue MG A 1307
08AC8SOFTWAREU A:1175 , HOH A:1421 , HOH A:1438 , HOH A:1441 , HOH A:1444binding site for residue MG A 1308
09AC9SOFTWAREG A:1157 , G A:1220 , HOH A:1415 , HOH A:1426 , HOH A:1452 , HOH A:1456binding site for residue MG A 1309
10AD1SOFTWAREG A:1223 , HOH A:1402 , HOH A:1430 , HOH A:1443 , HOH A:1450 , HOH A:1455 , HOH A:1458binding site for residue MG A 1310
11AD2SOFTWAREU A:1176 , A A:1177 , HOH A:1447binding site for residue NA A 1311
12AD3SOFTWAREG A:1169 , U A:1171binding site for residue NA A 1312
13AD4SOFTWAREA A:1179 , A A:1180 , C A:1182 , A A:1183 , MG A:1303 , HOH A:1401binding site for residue NA A 1313
14AD5SOFTWAREG A:1166 , A A:1167 , C A:1210binding site for residue TRS A 1314
15AD6SOFTWAREA A:1167 , G A:1168 , G A:1197 , G A:1199binding site for residue TRS A 1315
16AD7SOFTWAREASP B:34 , MSE B:36binding site for residue NA B 301
17AD8SOFTWAREGLU B:82 , ASN B:85 , TYR B:86binding site for residue TRS B 302
18AD9SOFTWARELYS C:110 , MSE C:113 , SER C:115 , HOH C:301 , HOH C:303binding site for residue MG C 201
19AE1SOFTWAREQUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12binding site for Ligand residues BB9 D 13 through NH2 D 18 bound to SER D 5
20AE2SOFTWAREA A:1177 , G A:1178 , A A:1205 , QUA D:0 , ALA D:4 , SER D:5 , DBU D:8 , DCY D:9 , THR D:12 , BB9 D:13binding site for Ligand residues BB9 D 6 through THR D 7 bound to SER D 5
21AE3SOFTWAREA A:1177 , A A:1205 , QUA D:0 , ALA D:4 , SER D:5 , THR D:7 , BB9 D:13binding site for Ligand BB9 D 6 bound to SER D 5
22AE4SOFTWAREALA D:4 , SER D:5 , BB9 D:13 , BB9 D:15binding site for Ligand MH6 D 14 bound to SER D 5
23AE5SOFTWAREA A:1177 , G A:1178 , LYS B:25 , GLU B:74 , PRO C:18 , QUA D:0 , THR D:7 , THR D:12binding site for Ligand residues DBU D 8 through BB9 D 11 bound to THR D 7
24AE6SOFTWAREQUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12 , MH6 D:14binding site for Ligand BB9 D 13 bound to THR D 12
25AE7SOFTWAREQUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12 , MH6 D:14binding site for Ligand BB9 D 13 bound to THR D 12

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D8H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly C:17 -Pro C:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D8H)

(-) Exons   (0, 0)

(no "Exon" information available for 5D8H)

(-) 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:RNA  Length:74
                                                                                                           
                5d8h A 1151 GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGCUCACCCGUCGAGGC 1224
                                  1160      1170      1180      1190      1200      1210      1220    


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee..hhhhhhhhhhhh.eee................ee.......hhhhh......eeee..eeee.............hhhhhhhhhhh....eee..eeeeeee..eeehhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d8h B    9 mAPWKIEEVKTLKGLIKSKPVVAIVDmmDVPAPQLQEIRDKIRDKVKLRmSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVTDmNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGmPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEE  215
                            |       18        28      ||38        48        58        68        78        88        98       108       118       128      |138       148       158       168       178       188       198       208       
                            9-MSE                    35-MSE                 58-MSE                                  98-MSE                              135-MSE                                                                            
                                                      36-MSE                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee........hhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeeeee.......eee...hhhhhhhh.................eehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...ee...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d8h C    1 AKEVVEVLVTGGRATAGPPLGPAIGPLGVNVmQVVKEINEKTKDYEGmQVPVKVIVDTETRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKmKKDAmLSYTLKNAVKEVLGTCGSmGVTVEGKDPKEVQKEIDAGVYDEYFK  158
                                    10        20        30 |      40       |50        60        70        80        90       100       110  |    120       130 |     140       150        
                                                          32-MSE          48-MSE                                                     108-MSE|                132-MSE                      
                                                                                                                                          113-MSE                                         


Chain D from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ................... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                5d8h D    0 xIAxASxTxxxxTxxxxxx   18
                            |  |  | |9|| ||||||
                            0-QUA | |||| |15-BB9
                               3-DHA|||| ||16-DHA
                                  6-BB9| || 17-DHA
                                    8-DBU||  18-NH2
                                     9-DCY|    
                                     10-TS9    
                                      11-BB9   
                                        13-BB9 
                                         14-MH6
   Legend:   → Mismatch (orange background)
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    → 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 5D8H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D8H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D8H)

(-) Gene Ontology  (13, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        RL10_METJA | P54049: 3jsy 5d6g 5dar
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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