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(-) Description

Title :  CRYSTAL STRUCTURE OF LARP1-UNIQUE DOMAIN DM15 BOUND TO M7GPPPC
 
Authors :  A. J. Berman, R. M. Lahr
Date :  21 Mar 17  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cap-Binding, Rna-Binding, Dm15, 5'Top, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. M. Lahr, B. D. Fonseca, G. E. Ciotti, H. A. Al-Ashtal, J. J. Jia, M. R. Niklaus, S. P. Blagden, T. Alain, A. J. Berman
La-Related Protein 1 (Larp1) Binds The Mrna Cap, Blocking Eif4F Assembly On Top Mrnas.
Elife V. 6 2017
PubMed-ID: 28379136  |  Reference-DOI: 10.7554/ELIFE.24146

(-) Compounds

Molecule 1 - LA-RELATED PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    GeneLARP1, KIAA0731, LARP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLA RIBONUCLEOPROTEIN DOMAIN FAMILY MEMBER 1

 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, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
191P1Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][[(2~{R},3~{S},4~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE
2MGT1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
191P-1Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][[(2~{R},3~{S},4~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE
2MGT1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
191P1Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-7-METHYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-IUM-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][[(2~{R},3~{S},4~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE
2MGT-1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:882 , TYR A:883 , GLU A:886 , GLU A:914 , LYS A:915 , ALA A:918 , TYR A:922 , HOH A:1103 , HOH A:1105 , HOH A:1126 , 91P B:1001binding site for residue MGT A 1001
2AC2SOFTWAREARG A:879 , TYR A:883 , TYR A:911 , GLU A:914 , LYS A:915 , MGT A:1001 , ARG B:847 , ARG B:879 , SER B:882 , TYR B:883 , GLU B:886 , GLU B:914 , LYS B:915 , ALA B:918 , TYR B:922 , HOH B:1106 , HOH B:1128 , HOH B:1144binding site for residue 91P B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V87)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V87)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V87)

(-) Exons   (0, 0)

(no "Exon" information available for 5V87)

(-) 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:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v87 A 794 HMQHPSHELLKEGFTQHVYHKYRRRCLNERKRLGIGQSQEMNTLFRFWSFFLRDHFNKKMYEEFKQLALEDAKEGYRYGLECLFRYYSYGLEKKFRLDIFKDFQEETVKDYEAGQLYGLEKFWAFLKYSKAKNLDIDPKLQEYLGKF 941
                                   803 ||    814       824       834       844       854       864       874       884       894       904       914       924       934       
                                     805|                                                                                                                                      
                                      807                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v87 B 794 HMQHPSHELLKENGFTQHVYHKYRRRCLNERKRLGIGQSQEMNTLFRFWSFFLRDHFNKKMYEEFKQLALEDAKEGYRYGLECLFRYYSYGLEKKFRLDIFKDFQEETVKDYEAGQLYGLEKFWAFLKYSKALDIDPKLQEYLGKFRL 944
                                   803       813       823       833       843       853       863       873       883       893       903       913       923 ||    935     || 
                                                                                                                                                             925|          941| 
                                                                                                                                                              928           943 

   Legend:   → Mismatch (orange background)
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  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 5V87)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V87)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V87)

(-) Gene Ontology  (19, 19)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LARP1_HUMAN | Q6PKG04zc4 5c0v 5v4r 5v7c

(-) Related Entries Specified in the PDB File

5v7c