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(-) Description

Title :  CORE OF MAMMALIAN 80S PRE-RIBOSOME IN COMPLEX WITH TRNAS FITTED TO A 10.6A CRYO-EM MAP: ROTATED PRE STATE 1
 
Authors :  T. Budkevich, J. Giesebrecht, R. Altman, J. Munro, T. Mielke, K. Nierha S. Blanchard, C. M. Spahn
Date :  06 Oct 11  (Deposition) - 16 Nov 11  (Release) - 16 Nov 11  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  10.60
Chains :  Asym./Biol. Unit :  B,G,L,S,W,X,Y,a,c,d,f,g,h,w,y,2,3,7
Keywords :  Mammalia, Translation, Elongation Cycle, Trna, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Budkevich, J. Giesebrecht, R. B. Altman, J. B. Munro, T. Mielke, K. H. Nierhaus, S. C. Blanchard, C. M. Spahn
Structure And Dynamics Of The Mammalian Ribosomal Pretranslocation Complex.
Mol. Cell V. 44 214 2011
PubMed-ID: 22017870  |  Reference-DOI: 10.1016/J.MOLCEL.2011.07.040

(-) Compounds

Molecule 1 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: a
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 2 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: c
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 3 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: d
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 4 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: g
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 5 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: G
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 6 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: f
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 7 - 40S RIBOSOMAL RNA FRAGMENT
    Chains: h
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 8 - RIBOSOMAL PROTEIN S15
    Chains: S
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 9 - RIBOSOMAL PROTEIN S23
    Chains: L
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 10 - RIBOSOMAL PROTEIN S30
    Chains: X
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 11 - 60S RIBOSOMAL RNA FRAGMENT
    Chains: 2
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 12 - 60S RIBOSOMAL RNA FRAGMENT
    Chains: 3
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 13 - 60S RIBOSOMAL RNA FRAGMENT
    Chains: 7
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 14 - RIBOSOMAL PROTEIN L10A
    Chains: B
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 15 - TRNA
    Chains: Y
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 16 - MRNA FRAGMENT
    Chains: y
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 17 - TRNA
    Chains: W
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER
 
Molecule 18 - MRNA FRAGMENT
    Chains: w
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: LIVER

 Structural Features

(-) Chains, Units

  123456789101112131415161718
Asymmetric/Biological Unit : BGLSWXYacdfghwy237

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3J0P)

(-) Sites  (0, 0)

(no "Site" information available for 3J0P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3J0P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu B:53 -Lys B:54
2Lys B:54 -Leu B:55
3Thr B:154 -Ile B:155
4Ile B:155 -Lys B:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J0P)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L1PS01199 Ribosomal protein L1 signature.RL1A_YEAST117-136  1B:117-136

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL220W1YPL220W.1XVI:135789-136442654RL1A_YEAST1-2172171B:4-216213

(-) 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 2 from PDB  Type:RNA  Length:112
                                                                                                                                                 
                3j0p 2 2194 GCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACG 2305
                                  2203      2213      2223      2233      2243      2253      2263      2273      2283      2293      2303  


Chain 3 from PDB  Type:RNA  Length:12
                                             
                3j0p 3 2477 GCCAGUGAAAUA 2488
                                  2486  


Chain 7 from PDB  Type:RNA  Length:50
                                                                                   
                3j0p 7 2824 GCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAU 2873
                                  2833      2843      2853      2863      2873


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with RL1A_YEAST | P0CX43 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:213
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   
          RL1A_YEAST      4 ITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRL  216
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh............................................................hhhhh...................hhhhhhhh......................hhhhhh............hhhhhh........................hhhhhhhhhhh.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBOSOMAL_L1        -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-216 UniProt: 1-217 [INCOMPLETE]                                                                                                                                                                    Transcript 1
                3j0p B    4 ITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRL  216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   


Chain G from PDB  Type:RNA  Length:13
                                              
                3j0p G 1429 GCACGCGCGUUAC 1441
                                  1438   


Chain L from PDB  Type:PROTEIN  Length:141
                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eeeeeeeeeeeee.......eeeeeeeee.....eeeee....hhhhh.....eeeeee...............eeeeee...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j0p L    2 GVGKPRGIRAGRKLARHRKDQRWADNDFNKRLLGSRWRNPFMGASHAKGLVTEKIGIESKQPNSAVRKCVRVLLRKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGVRFKVVCVKGISLLALFKGKKEKR  142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 


Chain S from PDB  Type:PROTEIN  Length:125
                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........eee.......hhhhh..eeeee....eeeee.hhhhh..hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                3j0p S   11 FTFRGKGLEELTALASGSNSEKLISDELAALFDAKTRRRVKRGISEKYAKFVNKVRRSKEKCPAGEKPVPVKTHYRSMIVIPELVGGIVGVYNGKEFVNVEVKFDMIGKYLAEFAMTYKPTTHGK  135
                                    20        30        40        50        60        70        80        90       100       110       120       130     


Chain W from PDB  Type:RNA  Length:77
                                                                                                              
                3j0p W    1 CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA   76
                                    10       |19        29        39        49        59        69       
                                           17A                                                           


Chain X from PDB  Type:PROTEIN  Length:68
                                                                                                     
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh..............hhhhhhhhhhhhh....................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                3j0p X    7 TLAKAGKVRKQTPKVEKKDKPRKTPKGRSYKRILYNRRYAPHILATDPKKRKSPNWHAGKKEKMDAAA   74
                                    16        26        36        46        56        66        


Chain Y from PDB  Type:RNA  Length:75
                                                                                                            
                3j0p Y    1 GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGCACC   75
                                    10        20        30        40        50        60        70     


Chain a from PDB  Type:RNA  Length:48
                                                                                 
                3j0p a  541 GGAGGGCAAGUCAUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUA  588
                                   550       560       570       580        


Chain c from PDB  Type:RNA  Length:17
                                                  
                3j0p c  972 GACGAUCAGAUACCGUC  988
                                   981       


Chain d from PDB  Type:RNA  Length:7
                                        
                3j0p d 1543 CGAGGAA 1549


Chain f from PDB  Type:RNA  Length:21
                                                      
                3j0p f 1236 GGUGGUGGUGCAUGGCCGUUC 1256
                                  1245 |||  1255 
                                    1247||       
                                     3248|       
                                      1249       


Chain g from PDB  Type:RNA  Length:31
                                                                
                3j0p g 1142 GAACCUGCGGCUUAAUUUGACUCAACACGGG 1172
                                  1151      1161      1171 


Chain h from PDB  Type:RNA  Length:111
                                                                                                                                                
                3j0p h 1606 CACCGCCCGUCGCUUGUAGUAACGAAUGGUCUGGUGAACCUUCUGGACUGCGACAGCAAUGUUGCGGAAAAAUAAGUAAACCCUACCAUUUGGAACAACAAGAAGUCGUAA 1716
                                  1615      1625      1635      1645      1655      1665      1675      1685      1695      1705      1715 


Chain w from PDB  Type:RNA  Length:2
                                   
                3j0p w   14 AA   15


Chain y from PDB  Type:RNA  Length:3
                                    
                3j0p y   19 UUC   21
   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 3J0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J0P)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (RL1A_YEAST | P0CX43)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0002181    cytoplasmic translation    The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
    GO:0000470    maturation of LSU-rRNA    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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    Ile B:155 - Lys B:156   [ RasMol ]  
    Leu B:53 - Lys B:54   [ RasMol ]  
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  RL1A_YEAST | P0CX43
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 Related Entries

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

UniProtKB/Swiss-Prot
        RL1A_YEAST | P0CX43: 1k5y 2noq 3j0q 3j6x 3j6y 3j77 3j78 4v4b 4v6i 4v7f 4v7h 4v7r 4v91 5jcs 5juo 5jup 5jus 5jut 5juu

(-) Related Entries Specified in the PDB File

3j0l 80S PRE-RIBOSOME CLASSIC PRE STATE 1
3j0o 80S PRE-RIBOSOME CLASSIC PRE STATE 2
3j0q 80S PRE-RIBOSOME ROTATED PRE STATE 2