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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR EF-1 BETA FROM PYROCOCCUS HORIKOSHII
 
Authors :  T. Ishii, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteo Initiative (Rsgi)
Date :  27 Apr 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Elongation Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ishii, Y. Bessho, S. Yokoyama
Crystal Structure Of Translation Elongation Factor Ef-1 Bet From Pyrococcus Horikoshii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ELONGATION FACTOR 1-BETA
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: EF-1-BETA, AEF-1BETA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YY3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YY3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YY3)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:91
 aligned with EF1B_PYRHO | P58748 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
            EF1B_PYRHO    1 MSDFNLVGVIRVMPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2yy3A00 A:2-91  [code=3.30.70.60, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.....hhhhhhhhhhhhh....eeeeeeeee.....eeeeeeeee......hhhhhhhhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2yy3 A  1 mSDFNLVGVIRVmPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
                            |       10  |     20        30        40        50        60        70        80        90 
                            |          13-MSE                                                                          
                            1-MSE                                                                                      


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with EF1B_PYRHO | P58748 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
            EF1B_PYRHO    1 MSDFNLVGVIRVMPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2yy3B00 B:2-91  [code=3.30.70.60, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.....hhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2yy3 B  1 mSDFNLVGVIRVmPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
                            |       10  |     20        30        40        50        60        70        80        90 
                            1-MSE      13-MSE                                                                          


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with EF1B_PYRHO | P58748 from UniProtKB/Swiss-Prot  Length:91

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
            EF1B_PYRHO    1 MSDFNLVGVIRVMPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2yy3C00 C:2-91  [code=3.30.70.60, no name defined]                                         CATH domains
           Pfam domains (1) EF1_GNE-2yy3C01 C:1-91                                                                      Pfam domains (1)
           Pfam domains (2) EF1_GNE-2yy3C02 C:1-91                                                                      Pfam domains (2)
           Pfam domains (3) EF1_GNE-2yy3C03 C:1-91                                                                      Pfam domains (3)
         Sec.struct. author .....eeeeeeeee......hhhhhhhhhh......eeeeeeeeeee..eeeeeeeeee......hhhhhhhhhh....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2yy3 C  1 mSDFNLVGVIRVmPTDPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFGLVALKFYVLGRDEEGYSFDEVAEKFEEVENVESAEVETVSRI 91
                            |       10  |     20        30        40        50        60        70        80        90 
                            1-MSE      13-MSE
   Legend:   → Mismatch (orange background)
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  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 2YY3)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: EF1_GNE] (1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (EF1B_PYRHO | P58748)
molecular function
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    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:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.

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