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(-) Description

Title :  HUMAN SERYL-TRNA SYNTHETASE DIMER COMPLEXED WITH TWO MOLECULES 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 :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D
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 - SERINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, C
    EC Number: 6.1.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B(+)
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: SARS, SERS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SERYL-TRNA SYNTHETASE, SERRS, SERYL-TRNA(SER/SEC) SYNTHETASE
 
Molecule 2 - SELENOCYSTEINE TRNA
    Chains: B, D
    Engineered: YES
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: IN VITRO SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

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
1AC1SOFTWARETHR A:271 , GLU A:273 , ARG A:302 , GLU A:325 , SER A:394 , ASN A:427 , THR A:429 , ANP A:602BINDING SITE FOR RESIDUE SER A 601
2AC2SOFTWAREARG A:302 , GLU A:304 , ARG A:317 , VAL A:318 , PHE A:321 , GLU A:391 , LEU A:392 , VAL A:393 , SER A:394 , THR A:429 , ALA A:432 , ARG A:435 , SER A:601BINDING SITE FOR RESIDUE ANP A 602
3AC3SOFTWARETHR C:271 , GLU C:325 , SER C:394 , ASN C:427 , THR C:429 , ANP C:602BINDING SITE FOR RESIDUE SER C 601
4AC4SOFTWAREARG C:302 , GLU C:304 , PHE C:316 , ARG C:317 , VAL C:318 , PHE C:321 , LYS C:376 , GLU C:391 , LEU C:392 , SER C:394 , THR C:429 , ALA C:432 , ARG C:435 , SER C:601BINDING SITE FOR RESIDUE ANP C 602

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:46 -A:117
2C:46 -C:117

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:417 -Asp A:418
2Met C:417 -Asp C:418

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RQE)

(-) 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhheeeeee.........hhhhhhhhh...hhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhh..eee...ee.hhhhhhh.hhhhhhhh..eeee...........eeeee...hhhhhhhhhh..........eeeeeeeeee..................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeee...........eeeeeeeee....eeee...eeeeehhhhhhh...........eeeeeeeee.hhhhhhhhhhh....eee...hhhhh.......eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqe A   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKELSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVTSIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPIEQES 601
                                    11        21        31        41        51        61        71||      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      |419       429       439       449       459       469       479|
                                                                                                 72|                                                                                                                                                                                                                                                                                                                                  410|                                                           479|
                                                                                                  85                                                                                                                                                                                                                                                                                                                                   417                                                            601


Chain B from PDB  Type:RNA  Length:84
                                                                                                                    
                 4rqe B   1 GGCCGGAUGAUCCUCAGUGGUCUGGGGUGCAGGCUAAACCUGUAGCUGUCUAGCGACAGAGUGGUUCAAUUCCACCUUUCGGGC  72
                                 ||  8       |19 |      28    ||  40       47C||||||||48|       59    || |68    
                                5A|         16|  |           33|         47A||||||47J||||            64| ||     
                                 5B          18  |            36          47B||||||47K|||             66 ||     
                                               20A                         47C||||||47L||              67A|     
                                                                            47D|||||  48|               67B     
                                                                             47E||||   50                       
                                                                              47F|||                            
                                                                               47G||                            
                                                                                47H|                            
                                                                                 47I                            


Chain C from PDB  Type:PROTEIN  Length:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhheeeeee.........hhhhhhhhh...hhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhh.hhhhhhhh..eeee...........eeee....hhhhhhhhhh..........eeeeeeeeee..................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeee...........eeeeeeeee....eeee...eeeeehhhhhhh...........eeeeeeeee.hhhhhhhhhhh....eee...hhhhh.......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqe C   2 VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKENVLSFDADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVTSIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAS 601
                                    11        21        31        41        51        61       |83    ||  96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406   ||  422       432       442       452       462       472 ||
                                                                                              69|    88|                                                                                                                                                                                                                                                                                                                           410|                                                      474|
                                                                                               82     92                                                                                                                                                                                                                                                                                                                            417                                                       601


Chain D from PDB  Type:RNA  Length:83
                                                                                                                   
                 4rqe D   1 GGCCGGAUGAUCCUCAGUGGUCUGGGGUGCAGGCUAAACCUGUAGCUGUCUAGCGACAGAGUGGUUCAAUUCCACCUUUCGGG  71
                                 ||  8       |19 |      28    ||  40       47C||||||||48|       59    || |68   
                                5A|         16|  |           33|         47A||||||47J||||            64| ||    
                                 5B          18  |            36          47B||||||47K|||             66 ||    
                                               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 4RQE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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    Met A:417 - Asp A:418   [ RasMol ]  
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  4rqe
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 Related Entries

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UniProtKB/Swiss-Prot
        SYSC_HUMAN | P49591: 3vbb 4l87 4rqf

(-) Related Entries Specified in the PDB File

4rqf