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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF SUP35 COMPLEXED WITH GDP
 
Authors :  C. Kong, H. Song
Date :  10 Oct 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Termination, Peptide Release, Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kong, K. Ito, M. A. Walsh, M. Wada, Y. Liu, S. Kumar, D. Barford, Y. Nakamura, H. Song
Crystal Structure And Functional Analysis Of The Eukaryotic Class Ii Release Factor Erf3 From S. Pombe
Mol. Cell V. 14 233 2004
PubMed-ID: 15099522  |  Reference-DOI: 10.1016/S1097-2765(04)00206-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP- BINDING SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21-STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 196-662
    Gene: SUP35
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: ERF2, TRANSLATION RELEASE FACTOR 3, ERF3, ERF-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:246 , VAL A:247 , ASP A:248 , ALA A:249 , GLY A:250 , LYS A:251 , SER A:252 , THR A:253 , LYS A:278 , ASN A:384 , LYS A:385 , ASP A:387 , GLU A:388 , SER A:427 , ALA A:428 , TYR A:429BINDING SITE FOR RESIDUE GDP A 663

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R5N)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:502 -Pro A:503

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R5N)

(-) Exons   (0, 0)

(no "Exon" information available for 1R5N)

(-) 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:PROTEIN  Length:408
 aligned with ERF3_SCHPO | O74718 from UniProtKB/Swiss-Prot  Length:662

    Alignment length:448
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654        
           ERF3_SCHPO   215 TEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGMVDKRTMEKIEREAKEAGKESWYLSWALDSTSEEREKGKTVEVGRAYFETEHRRFSLLDAPGHKGYVTNMINGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRKSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD 662
               SCOP domains d1r5na3 A:215-459 Eukaryotic peptide chain release factor ERF2,                              G domain                                                                                                                                                d1r5na1 A:460-554 Eukaryotic peptide chain release factor ERF2, post-G domain                  d1r5na2 A:555-622                                                   ---------------------------------------- SCOP domains
               CATH domains 1r5nA01 A:215-463 P-loop containing nucleotide triphosphate hydr                             olases                                                                                                                                                      1r5nA02 A:464-552 Translation factors                                                    1r5nA03 A:553-662 Translation factors                                                                          CATH domains
           Pfam domains (1) ---------------------GTP_EFTU-1r5nA01 A:236-484                                                                                                                                                                                                                               --------------------------------------------------------------------GTP_EFTU_D3-1r5nA03 A:553-661                                                                                - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_EFTU_D2-1r5nA02 A:481-548                                       ------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......hhhhh...........eeeeeeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhh-----------------------------..eee...eeeeee...-----------......eeeeeee...hhhhhh.....hhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhhhhh.......eeee........................hhhhhhhhh..hhhhhh...eee..eeee...eeeeee....ee....eeeee...eeeeeeeee.....ee..ee...eeeeeee..........eee......eeeeeeeeeeee...........eeee......eeeeeeeeeee...................eeeeeeeeeeeeee.....hhhh.eeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5n A 215 TEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGMVDKRTMEKIEREAK-----------------------------RAYFETEHRRFSLLDAP-----------GASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRKSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD 662
                                   224       234       244       254       264       274   |     -         -         -   |   314       324         - |     344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654        
                                                                                         278                           308             324         336
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTP_EFTU_D2] (39)
(-)
Clan: no clan defined [family: GTP_EFTU_D3] (11)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERF3_SCHPO | O74718)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
biological process
    GO:0002184    cytoplasmic translational termination    The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    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:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0018444    translation release factor complex    A heterodimeric complex involved in the release of a nascent polypeptide chain from a ribosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ERF3_SCHPO | O74718: 1r5b 1r5o 3e20

(-) Related Entries Specified in the PDB File

1r5b THE SAME PROTEIN WITHOUT LIGAND
1r5o THE SAME PROTEIN COMPLEXED WITH GMPPNP