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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN EEFSEC IN COMPLEX WITH GDPCP
 
Authors :  M. Dobosz-Bartoszek, M. Simonovic
Date :  25 Mar 16  (Deposition) - 12 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Elongation Factor, Selenocysteine, Selenocysteine Trna, Translation, Gtpase, Gdpcp, Gtp (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Dobosz-Bartoszek, M. H. Pinkerton, Z. Otwinowski, S. Chakravarthy, D. Soll, P. R. Copeland, M. Simonovic
Crystal Structures Of The Human Elongation Factor Eefsec Suggest A Non-Canonical Mechanism For Selenocysteine Incorporation.
Nat Commun V. 7 12941 2016
PubMed-ID: 27708257  |  Reference-DOI: 10.1038/NCOMMS12941

(-) Compounds

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneEEFSEC, SELB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymELONGATION FACTOR SEC,EUKARYOTIC ELONGATION FACTOR, SELENOCYSTEINE-TRNA-SPECIFIC

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GCP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GCP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GCP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:21 , THR A:48 , GCP A:1002 , HOH A:1104 , HOH A:1105binding site for residue MG A 1001
2AC2SOFTWAREILE A:16 , ASP A:17 , SER A:18 , GLY A:19 , LYS A:20 , THR A:21 , ALA A:22 , GLU A:44 , ILE A:47 , THR A:48 , GLY A:95 , ASN A:146 , LYS A:147 , ASP A:149 , LEU A:150 , ALA A:186 , LYS A:187 , PRO A:188 , PRO A:191 , MG A:1001 , HOH A:1104 , HOH A:1105 , HOH A:1110binding site for residue GCP A 1002
3AC3SOFTWARETHR B:21 , GLY B:46 , THR B:48 , GCP B:1002 , HOH B:1106binding site for residue MG B 1001
4AC4SOFTWAREILE B:16 , ASP B:17 , SER B:18 , GLY B:19 , LYS B:20 , THR B:21 , ALA B:22 , ILE B:47 , THR B:48 , ASN B:146 , LYS B:147 , ASP B:149 , LEU B:150 , ALA B:185 , ALA B:186 , LYS B:187 , PRO B:191 , MG B:1001 , HOH B:1106binding site for residue GCP B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IZL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IZL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IZL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IZL)

(-) Exons   (0, 0)

(no "Exon" information available for 5IZL)

(-) 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:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....hhhhhhhhhhhhh.........eeeeeeee.hhhhhhhh.....eeeeeeee...hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhh.........eee.............hhhhhhhhhhhhh...........eeeeeeeee.....eeeeeeeee.eee...eee......eeeeeeeee..ee..eee...eeeeee...hhhhh..eeee.....eeeeeeee..ee............eeeeee..eeeeee..eeee.hhhh.............eeeee.............eeeeeeeeeeee....eeeee........eeeeeeeeeee...hhhhhhhhhheeeeeeeeeeeeee.....eeeee.......hhhhhh..eeee....eeee........ee.....hhhhhhh.....eeeeeeee..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izl A   2 AGRRVNVNVGVLGHIDSGKTALARALSTTARERGITLDLGFSCFSVPLPARLRSSLPPGEPLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGPTEAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSKGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDTNTCRLAFHGILLHGLEDRNYADSFLPRLKVYKLKHKHGLVERAMDDYSVIGRSLFKKETNIQLFVGLKVHLSTGELGIIDSAFGKFKIHIPGGLSPESKKIEPSQHVVLSLTFKRYVFDTHKRMVQS 595
                                    11        21        31|       52        62      ||83        93       103       113       123       133       143       153       163       173       183       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377    || 408       418       428     ||442       452       462       472       482       492       502       512       522||     535       571       581       591    
                                                        31|                        69|                                                                                                           191|                                                                                                                                                                                       382|                           434|                                                                                 523|             543|                         
                                                         43                         81                                                                                                            196                                                                                                                                                                                        404                            439                                                                                  527              570                         

Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee....hhhhhhhhhhhhh........eeeeeeee.hhhhh.......eeeeeeee...hhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh........eee..............hhhhhhhhhhhhh...........eeeeeeeeee...eeeeeeeeee.......eeeehhhheeeeeeeeee..eee.......eeeeee...hhhhh..eeee.....eeeeeeee..ee............eeeeee..eeeeeeeeeeee.hhhh.............eeee..............eeeeeeeeeeee....eeeee............eeeeeeeeeee...hhhhhhhhhheeee.............hhhhhh..eeee...eeeee......ee.....hhhhhh...ee...eee.........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5izl B   2 AGRRVNVNVGVLGHIDSGKTALARALSTTASRGITLDLGFSCFSVPLPARLRSSLPGEPLLQVTLVDCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGPETEAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSKGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGILLHGLEDRNYADSFLPRLKVYKLKHKRAMDDYSVINIQLFVGLKVHLSTGELGIIDSGKFKIHIPGGLSPESKKILHVVLSLTFKRYVFDTHKRMVQS 595
                                    11        21        31||      53        63    ||  85        95       105       115       125       135       145       155       165       175       185     ||198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   ||  409       419       429       439       449       459       469     ||484    || 503       513      |528       538     ||577       587        
                                                         32|                     68|                                                                                                           191|                                                                                                                                                                                        382|                                                                    475|     489|                  520|               544|                     
                                                          45                      81                                                                                                            195                                                                                                                                                                                         404                                                                     481      499                   526                574                     

   Legend:   → Mismatch (orange background)
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    → 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 5IZL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IZL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IZL)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        SELB_HUMAN | P577725izk 5izm

(-) Related Entries Specified in the PDB File

5izk 5izm