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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIBOSOMAL PROTEIN L10 CORE DOMAIN
 
Authors :  M. Nishimura, T. Kaminishi, C. Takemoto, M. Kawazoe, T. Yoshida, A. Tanaka, S. Sugano, M. Shirouzu, T. Ohkubo, S. Yokoyama, Y. Kobayashi, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Mar 07  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosomal Protein L10, Qm Protein, , Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Nishimura, T. Kaminishi, C. Takemoto, M. Kawazoe, T. Yoshida, A. Tanaka, S. Sugano, M. Shirouzu, T. Ohkubo, S. Yokoyama, Y. Kobayashi
Crystal Structure Of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs In Addition To The Conserved Fold
J. Mol. Biol. V. 377 421 2008
PubMed-ID: 18258260  |  Reference-DOI: 10.1016/J.JMB.2008.01.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 60S RIBOSOMAL PROTEIN L10
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET32B-L10CD
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCORE DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymQM PROTEIN, TUMOR SUPPRESSOR QM, LAMININ RECEPTOR HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:156 , PHE A:159 , GLY A:161 , GLN A:163 , HOH A:199BINDING SITE FOR RESIDUE K A 1
2AC2SOFTWARELYS B:156 , PHE B:159 , GLY B:161 , GLN B:163BINDING SITE FOR RESIDUE K B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PA2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:92 -Pro A:93
2His B:92 -Pro B:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PA2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L10EPS01257 Ribosomal protein L10e signature.RL10_HUMAN108-129
 
  2A:124-129
B:124-129
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L10EPS01257 Ribosomal protein L10e signature.RL10_HUMAN108-129
 
  1A:124-129
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L10EPS01257 Ribosomal protein L10e signature.RL10_HUMAN108-129
 
  1-
B:124-129

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4cENST000003447464cENSE00001450984X:153626713-153626883171RL10_HUMAN1-880--
1.6aENST000003447466aENSE00001718945X:153627679-15362773759RL10_HUMAN8-28210--
1.6eENST000003447466eENSE00001771764X:153627828-153627935108RL10_HUMAN28-64372A:40-64
B:40-64
25
25
1.6fENST000003447466fENSE00001200803X:153628144-153628282139RL10_HUMAN64-110472A:64-94
B:64-94
31
31
1.6lENST000003447466lENSE00001391300X:153628805-153628967163RL10_HUMAN110-164552A:124-164
B:124-164
41
41
1.6sENST000003447466sENSE00001216995X:153629043-1536306801638RL10_HUMAN165-214502A:165-176
B:165-176
12
12

(-) 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:108
 aligned with RL10_HUMAN | P27635 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:137
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       
           RL10_HUMAN    40 KAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKF 176
               SCOP domains d2pa2a1 A:40-176 Ribosomal protein L10e                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee...eeeehhhhhhhhhhhhhhhhhhhh...eeeee.....-----------------------------..eeee....eeeeeee...hhhhhhhhhhhhhhhh...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------RIBOSOMAL_L10E        ----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6e  PDB: A:40-64  ---------------------------------------------Exon 1.6l  PDB: A:124-164 UniProt: 110-164 [INCOMPLETE]Exon 1.6s    Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.6f  PDB: A:64-94 UniProt: 64-110        ------------------------------------------------------------------ Transcript 1 (2)
                 2pa2 A  40 KAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPF-----------------------------GTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKF 176
                                    49        59        69        79        89    |    -         -         -    |  129       139       149       159       169       
                                                                                 94                           124                                                    

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with RL10_HUMAN | P27635 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:137
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       
           RL10_HUMAN    40 KAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKF 176
               SCOP domains d2pa2b1 B:40-176 Ribosomal protein L10e                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ribosomal_L16-2pa2B01 B:40-167                                                                                                  --------- Pfam domains (1)
           Pfam domains (2) Ribosomal_L16-2pa2B02 B:40-167                                                                                                  --------- Pfam domains (2)
         Sec.struct. author ........eeeeeee...eeeehhhhhhhhhhhhhhhhhhhh...eeeee.....-----------------------------..eeee....eeeeeee...hhhhhhhhhhhhhhhh...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------RIBOSOMAL_L10E        ----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6e  PDB: B:40-64  ---------------------------------------------Exon 1.6l  PDB: B:124-164 UniProt: 110-164 [INCOMPLETE]Exon 1.6s    Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.6f  PDB: B:64-94 UniProt: 64-110        ------------------------------------------------------------------ Transcript 1 (2)
                 2pa2 B  40 KAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHPF-----------------------------GTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKF 176
                                    49        59        69        79        89    |    -         -         -    |  129       139       149       159       169       
                                                                                 94                           124                                                    

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PA2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RL10_HUMAN | P27635)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006614    SRP-dependent cotranslational protein targeting to membrane    The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0000027    ribosomal large subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
    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.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        RL10_HUMAN | P276355aj0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PA2)