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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ARGRS-GLNRS-AIMP1 COMPLEX
 
Authors :  Y. Fu, Y. Kim, Y. Cho
Date :  18 Aug 14  (Deposition) - 08 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.03
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Amino-Acyl Trna Synthetase Complex, Multi-Synthetase Complex, Ligation Amino Acid To Trna, Protein Binding-Ligase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fu, Y. Kim, K. S. Jin, H. S. Kim, J. H. Kim, D. M. Wang, M. Park, C. H. Jo, N. H. Kwon, D. Kim, M. H. Kim, Y. H. Jeon, K. Y. Hwang, S. Kim, Y. Cho
Structure Of The Argrs-Glnrs-Aimp1 Complex And Its Implications For Mammalian Translation
Proc. Natl. Acad. Sci. Usa V. 111 15084 2014
PubMed-ID: 25288775  |  Reference-DOI: 10.1073/PNAS.1408836111

(-) Compounds

Molecule 1 - AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AIMP1, EMAP2, SCYE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P43, ENDOTHELIAL MONOCYTE-ACTIVATING POLYPEPTIDE 2, EMAP-2, ENDOTHELIAL MONOCYTE- ACTIVATING POLYPEPTIDE II, EMAP-II, SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1
 
Molecule 2 - ARGININE--TRNA LIGASE, CYTOPLASMIC
    Chains: B
    EC Number: 6.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARGINYL-TRNA SYNTHETASE, ARGRS
 
Molecule 3 - GLUTAMINE--TRNA LIGASE
    Chains: C
    EC Number: 6.1.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: QARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLUTAMINYL-TRNA SYNTHETASE, GLNRS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4R3Z)

(-) Sites  (0, 0)

(no "Site" information available for 4R3Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3Z)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Ile A:78 -Pro A:79
2Pro A:79 -Phe A:80
3Pro B:69 -Thr B:70
4Ser B:105 -Gln B:106
5Phe B:452 -Lys B:453
6Ser B:456 -Gly B:457
7Glu B:479 -Lys B:480
8Lys B:620 -Asp B:621
9Ile B:627 -Leu B:628
10Arg C:361 -Gly C:362
11Ala C:609 -Pro C:610
12Gly C:709 -Gly C:710
13Ser C:719 -Leu C:720
14Leu C:720 -His C:721
15Val C:732 -Ala C:733
16Ala C:733 -Leu C:734

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3Z)

(-) 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:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4r3z A   5 DAVLKRLEQKGAEADQIIEYLKQQVSLLKEKAILQATLREEKKLRVENAKLKKEIEELKQELIQAEIQNGVKQIPF  80
                                    14        24        34        44        54        64        74      


Chain B from PDB  Type:PROTEIN  Length:659
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhhhhhh................hhhhhhhhhh.........ee.........eee..hhhhhh.........hhhhhhhhhhh.......eeeeee.....eeeeehhhhhhhhhhhhhhh...........eeeee...........hhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeee..eeee........eeee.........hhhhhh.hhhhhh....eeeee....hhhhhhhhhhhhhhhh.........eee....ee...............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee............hhhhhhhhhhh....hhhhh..................hhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3z B   2 DVLVSECSARLLQQEEEIKSLTAEIDRLKNCGCLGASPNLEQLQEENLKLKYRLNILRKSLQAERNKPTKNMINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKTKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALGENKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTRSGETVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSHNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVEKDRQTGKILKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRM 660
                                    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       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651         


Chain C from PDB  Type:PROTEIN  Length:538
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...................hhhhhhhhhh........eee........hhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhh..ee..................hhhhhhhhhhhhhhh.........ee...........eee.............eeehhhhhhhhhhhhh.............hhhhhhhhh.......................hhhhhhhhhhhh...........hhhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhhh.......ee..eeeeee...........eee.......eee......eeee.hhh................ee......ee....ee........eeee......................eee............................ee...ee..........eee....eeeee.........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3z C 220 LMEQLRGEALKFHKPGENYKTPGYVVTPHTMNLLKQHLEITGGQVRTRFPPEPNGILHIGHAKAINFNFGYAKANNGICFLRFDDTNPEKEEAKFFTAICDMVAWLGYTPYKVTYASDYFDQLYAWAVELIRRGLAYVCHQRGEELKLPSPWRDRPMEESLLLFEAMRKGKFSEGEATLRMKLVMGKMDPVAYRVKYTPHHRTGDKWCIYPTYDYTHCLCDSIEHITHSLCTKEFQARRSSYFWLCNALDVYCPVQWEYGRLNLHYAVVSKRKILQLVATGAVRDWDDPRLFTLTALRRRGFPPEAINNFCARVGVTVAQTTMEPHLLEACVRDVLNDTAPRAMAVLESLRVIITNFPAAKSLDIQVPNFPADEGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPFIHWVSQPLMCEVRLYERLFQHEDPTEVPGGFLSDLNLASLHVVDAALVDCSVALAPFDKFQFERLGYFSVDPDSHQGKLVFNRTVTLKED 771
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359      |373       383       393       403    || 415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595   ||  607       617       627       637       647       657       667      |679       689       702       712       722       732  ||   743       753       763        
                                                                                                                                                                            366|                                  408|                                                                                                                                                                                         599|                                                                     674|                  698|                              735|                                  
                                                                                                                                                                             371                                   411                                                                                                                                                                                          602                                                                      677                   702                               737
   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 4R3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3Z)

(-) Gene Ontology  (50, 69)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4r3z)
 
  Cis Peptide Bonds
    Ala C:609 - Pro C:610   [ RasMol ]  
    Ala C:733 - Leu C:734   [ RasMol ]  
    Arg C:361 - Gly C:362   [ RasMol ]  
    Glu B:479 - Lys B:480   [ RasMol ]  
    Gly C:709 - Gly C:710   [ RasMol ]  
    Ile A:78 - Pro A:79   [ RasMol ]  
    Ile B:627 - Leu B:628   [ RasMol ]  
    Leu C:720 - His C:721   [ RasMol ]  
    Lys B:620 - Asp B:621   [ RasMol ]  
    Phe B:452 - Lys B:453   [ RasMol ]  
    Pro A:79 - Phe A:80   [ RasMol ]  
    Pro B:69 - Thr B:70   [ RasMol ]  
    Ser B:105 - Gln B:106   [ RasMol ]  
    Ser B:456 - Gly B:457   [ RasMol ]  
    Ser C:719 - Leu C:720   [ RasMol ]  
    Val C:732 - Ala C:733   [ RasMol ]  
 

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  4r3z
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  AIMP1_HUMAN | Q12904
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  SYRC_HUMAN | P54136
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  6.1.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        AIMP1_HUMAN | Q12904: 1e7z 1euj 1fl0
        SYQ_HUMAN | P47897: 4ye6 4ye8 4ye9
        SYRC_HUMAN | P54136: 4q2t 4q2x 4q2y 4zaj

(-) Related Entries Specified in the PDB File

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