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(-) Description

Title :  HUMAN SERYL-TRNA SYNTHETASE DIMER COMPLEXED WITH ONE MOLECULE OF TRNASEC
 
Authors :  W. Xie, C. Wang, Y. Guo, Q. Tian, Q. Jia
Date :  03 Nov 14  (Deposition) - 04 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Aminoacyl-Trna Synthetase, Classii Aars, Aminoacylation, Serine, Cytosol, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Wang, Y. Guo, Q. Tian, Q. Jia, Y. Gao, Q. Zhang, C. Zhou, W. Xie
Serrs-Trna Sec Complex Structures Reveal Mechanism Of The First Step In Selenocysteine Biosynthesis
Nucleic Acids Res. 2015
PubMed-ID: 26433229  |  Reference-DOI: 10.1093/NAR/GKV996

(-) Compounds

Molecule 1 - SELENOCYSTEINE TRNA
    ChainsC
    EngineeredYES
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsIN VITRO SYNTHESIS
    SyntheticYES
 
Molecule 2 - SERINE--TRNA LIGASE, CYTOPLASMIC
    ChainsA, B
    EC Number6.1.1.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET20B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET
    GeneSARS, SERS
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERYL-TRNA SYNTHETASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2SER2Mod. Amino AcidSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:317 , VAL A:318 , PHE A:321 , LEU A:392 , SER A:394 , ALA A:432 , ARG A:435 , SER A:601BINDING SITE FOR RESIDUE ANP A 602
2AC2SOFTWARETHR A:271 , GLU A:273 , GLU A:325 , ASN A:427 , ALA A:428 , THR A:429 , ANP A:602BINDING SITE FOR RESIDUE SER A 601
3AC3SOFTWARETHR B:271 , GLU B:273 , LYS B:323 , SER B:394 , ASN B:427 , THR B:429 , ANP B:602BINDING SITE FOR RESIDUE SER B 601
4AC4SOFTWAREARG B:317 , VAL B:318 , PHE B:321 , LEU B:392 , ALA B:432 , ARG B:435 , SER B:601BINDING SITE FOR RESIDUE ANP B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RQF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:417 -Asp A:418
2Asp B:161 -Cys B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RQF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RQF)

(-) Exons   (0, 0)

(no "Exon" information available for 4RQF)

(-) 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:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhh..eeee...ee.hhhhhhhhhhhhhhhh..eeee...........eeeee...hhhhhhhhhh..ee......eeeeeeeeee..................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhh..ee...........eeeeeeeehhhhhhhhhhhhh....eee...hhhhh.......eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqf A   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTMMDKVEFVHMLNATMCATTRTICAILENYQTKKGITVPEKLKEFMPPGLQELIPFVKPAPI 476
                                    11        21        31        41        51        61  ||    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413|      425       435       445       455       465       475 
                                                                                         64|                                                                                                                                                                                                                                                                                                                                   413|                                                            
                                                                                          87                                                                                                                                                                                                                                                                                                                                    416                                                            

Chain B from PDB  Type:PROTEIN  Length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhheeeeee.........hhhhhhhhh..eehhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhhhhhhhhhhh.eeeee...........eeeee...hhhhhhh....ee.......eeeeeeeeee..................eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhhhee..............eeeeeeeehhhhhhhhhhhhh....eee.hhhhhh........eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqf B   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTKKGITVPEKLKEFMPPGLQELIPFVKPAPS 601
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471   ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   475|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    601

Chain C from PDB  Type:RNA  Length:63
                                                                                               
                 4rqf C   5 GGAUGAUCCUCAGUGGUCUGGGGUGCAAGCUGUCUAGCGACAGAGUGGUUCAAUUCCACCUUU 67B
                             ||     12   ||  |22      ||46 ||||||47I|||||   55        66 ||
                             ||         16|  |       29| 47A||||||47J||||            64| ||
                            5A|          18  |        44  47B||||||47K|||             66 ||
                             5B            20A             47C||||||47L||              67A|
                                                            47D|||||  48|               67B
                                                             47E||||   50                  
                                                              47F|||                       
                                                               47G||                       
                                                                47H|                       
                                                                 47I                       

   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  (0, 0)

(no "SCOP Domain" information available for 4RQF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RQF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RQF)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp B:161 - Cys B:162   [ RasMol ]  
    Met A:417 - Asp A:418   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYSC_HUMAN | P495913vbb 4l87 4rqe

(-) Related Entries Specified in the PDB File

4rqe