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Title :  CRYSTAL STRUCTURE OF THE AIMP3-MRS N-TERMINAL DOMAIN COMPLEX
 
Authors :  H. Y. Cho, W. W. Seo, H. J. Cho, B. S. Kang
Date :  29 Jun 13  (Deposition) - 16 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase-Translation Complex, Aimp3, Mrs (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Y. Cho, W. W. Seo, H. J. Cho, B. S. Kang
Crystal Structure Of The Aimp3-Mrs N-Terminal Domain Comple
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE--TRNA LIGASE, CYTOPLASMIC
    ChainsA
    EC Number6.1.1.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA 2
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-225
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMETHIONYL-TRNA SYNTHETASE, METRS
 
Molecule 2 - EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-174
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsM1 TO H174 OF AIMP3 WITH ADDITIONAL S SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE
    SynonymAIMP3 AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 3, ELONGATION FACTOR P18, MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P18

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4BVY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:48 -Pro A:49
2Asn B:36 -Asp B:37
3Asp B:37 -Gly B:38
4Lys B:166 -Asn B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077848V5MSYMC_HUMANUnclassified587777227AV5M
2UniProtVAR_075360P206LSYMC_HUMANPolymorphism138776588AP206L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.MCA3_HUMAN50-173  1B:50-167
SYMC_HUMAN74-198  1A:74-198

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002620271aENSE00001341718chr12:57881851-57881982132SYMC_HUMAN1-37371A:1-3737
1.2ENST000002620272ENSE00001274042chr12:57882802-5788289291SYMC_HUMAN37-67311A:37-6731
1.3ENST000002620273ENSE00001273905chr12:57883050-5788312879SYMC_HUMAN67-93271A:67-9327
1.4ENST000002620274ENSE00001274065chr12:57883207-57883341135SYMC_HUMAN94-138451A:94-13845
1.5ENST000002620275ENSE00001273978chr12:57883679-5788375476SYMC_HUMAN139-164261A:139-16426
1.6ENST000002620276ENSE00001273945chr12:57883990-57884162173SYMC_HUMAN164-221581A:164-21148
1.7bENST000002620277bENSE00001273888chr12:57884321-57884427107SYMC_HUMAN222-257360--
1.8ENST000002620278ENSE00001108429chr12:57891940-57892056117SYMC_HUMAN257-296400--
1.9ENST000002620279ENSE00001024050chr12:57892203-57892406204SYMC_HUMAN296-364690--
1.10ENST0000026202710ENSE00001024092chr12:57894104-57894305202SYMC_HUMAN364-431680--
1.11ENST0000026202711ENSE00001024045chr12:57898008-5789808275SYMC_HUMAN432-456250--
1.12ENST0000026202712ENSE00001273848chr12:57905481-57905651171SYMC_HUMAN457-513570--
1.13aENST0000026202713aENSE00001024125chr12:57905791-5790588696SYMC_HUMAN514-545320--
1.14ENST0000026202714ENSE00001024043chr12:57906019-57906136118SYMC_HUMAN546-585400--
1.15aENST0000026202715aENSE00001273818chr12:57906534-57906747214SYMC_HUMAN585-656720--
1.16ENST0000026202716ENSE00001273812chr12:57908503-57908634132SYMC_HUMAN656-700450--
1.17ENST0000026202717ENSE00001139685chr12:57908737-57908841105SYMC_HUMAN700-735360--
1.18ENST0000026202718ENSE00001139676chr12:57908933-57909119187SYMC_HUMAN735-797630--
1.19ENST0000026202719ENSE00001139670chr12:57909703-5790977472SYMC_HUMAN798-821240--
1.20ENST0000026202720ENSE00001273921chr12:57910028-5791012093SYMC_HUMAN822-852310--
1.21ENST0000026202721ENSE00001274018chr12:57910218-57910433216SYMC_HUMAN853-900480--

(-) 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:211
 aligned with SYMC_HUMAN | P56192 from UniProtKB/Swiss-Prot  Length:900

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SYMC_HUMAN     1 MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPEDCVVPFLTRPKVPVLQLDSGNYLFSTSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRALTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHSWFQTLSTQEPCQRAAETVLKQQGVLALRPYLQKQPQPSPA 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh.....eeee.................eee.....ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----M--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------GST_CTER  PDB: A:74-198 UniProt: 74-198                                                                                      ------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-37 UniProt: 1-37 -----------------------------Exon 1.3  PDB: A:67-93     Exon 1.4  PDB: A:94-138 UniProt: 94-138      Exon 1.5  PDB: A:139-164  ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.2  PDB: A:37-67         ------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:164-211 UniProt: 164-221        Transcript 1 (2)
                 4bvy A   1 MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPQDCVVPFLTRPKVPVLQLDSGNYLFSTSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRALTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHSWFQTLSTQEPCQRAAQTVLKQQGVLALRPYLQKQPQPSPA 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with MCA3_HUMAN | O43324 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
           MCA3_HUMAN     - -MAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKN 167
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh......eeee....eeeee.....eeehhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------GST_CTER  PDB: B:50-167 UniProt: 50-173                                                                                PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bvy B   0 SMAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNDGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFSHIQHYPGIRQHLSSVVFIKN 167
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        

   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 4BVY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYMC_HUMAN | P56192)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0004825    methionine-tRNA ligase activity    Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006431    methionyl-tRNA aminoacylation    The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    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.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (MCA3_HUMAN | O43324)
molecular function
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0043517    positive regulation of DNA damage response, signal transduction by p53 class mediator    Any process that activates, maintains or increases the rate of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:2000774    positive regulation of cellular senescence    Any process that activates or increases the frequency, rate or extent of cellular senescence.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    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:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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    Asn B:36 - Asp B:37   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        MCA3_HUMAN | O433242uz8 4bl7 4bvx 5bmu
        SYMC_HUMAN | P561922djv 4bl7 4bvx 5gl7

(-) Related Entries Specified in the PDB File

4bvx CRYSTAL STRUCTURE OF THE AIMP3-MRS N-TERMINAL DOMAIN COMPLEX WITH I3C