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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIBOSOME MATURATION FACTOR RIMM (HI0203) FROM H.INFLUENZAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET IR66.
 
Authors :  A. Kuzin, M. Su, J. Seetharaman, M. Mao, R. Xiao, M. Maglaqui, L. Zhao, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  30 Apr 09  (Deposition) - 19 May 09  (Release) - 19 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Crystal Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Ir66, Rimm, Chaperone, Cytoplasm, Ribosome Biogenesis, Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kuzin, M. Su, J. Seetharaman, M. Mao, R. Xiao, M. Maglaqui, L. Zhao, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Northeast Structural Genomics Consortium Target Ir66
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME MATURATION FACTOR RIMM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HI0203, RIMM
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 21)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:147 , GLY A:177 , PHE A:178BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWARETYR A:19 , ARG A:60 , HIS A:62BINDING SITE FOR RESIDUE SO4 A 2
3AC3SOFTWARELYS A:147 , ARG A:150 , LEU A:151 , TRP A:174BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREGLY A:146 , LYS A:147 , GLN A:148 , GLU A:149BINDING SITE FOR RESIDUE SO4 A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H9N)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:41 -Pro A:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H9N)

(-) Exons   (0, 0)

(no "Exon" information available for 3H9N)

(-) 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:177
 aligned with RIMM_HAEIN | P44568 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:177
                                                                                                                                                                                                    178      
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177|      
           RIMM_HAEIN     8 HIEVVGKLGSTYGIRGWLRIYSSTEQAESIFDYQPWFLKIKGEWQSIELENWRYHNHEIIVKLKGVDDREAAQILANVEIGVDLSVFPELEEGDYYWHDLIGCTVVNLEGYTMGTVTEMMETGSNDVLVVKANTKDAFGKQERLIPFLYEQVVKRVDLTTKTIEVDWDAGF------   -
               SCOP domains d3h9na1 A:8-101 automated matches                                                             d3h9na2 A:102-184 automated matches                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......eeeee....hhhhhhh..eeeee..eeeee.eeeeee....eeeee....hhhhhhh....eeeee..........hhhhhhh...eeee....eeeeeeeeee....eeeeee..........eeeee......eeeeehhh.eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h9n A   8 HIEVVGKLGSTYGIRGWLRIYSSTEQAESIFDYQPWFLKIKGEWQSIELENWRYHNHEIIVKLKGVDDREAAQILANVEIGVDLSVFPELEEGDYYWHDLIGCTVVNLEGYTmGTVTEmmETGSNDVLVVKANTKDAFGKQERLIPFLYEQVVKRVDLTTKTIEVDWDAGFLEHHHH 184
                                    17        27        37        47        57        67        77        87        97       107       117  |    127       137       147       157       167       177       
                                                                                                                                          120-MSE ||                                                         
                                                                                                                                                126-MSE                                                      
                                                                                                                                                 127-MSE
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H9N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H9N)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIMM_HAEIN | P44568)
molecular function
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    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:0042274    ribosomal small subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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)

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(-) Related Entries Specified in the PDB File

ir66