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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO2 MID DOMAIN
 
Authors :  F. Frank, J. Hauver, N. Sonenberg, B. Nagar
Date :  09 Jul 12  (Deposition) - 25 Jul 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mid Domain, Small Rna 5' Nucleotide Recognition, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Frank, J. Hauver, N. Sonenberg, B. Nagar
Arabidopsis Argonaute Mid Domains Use Their Nucleotide Specificity Loop To Sort Small Rnas.
Embo J. V. 31 3588 2012
PubMed-ID: 22850669  |  Reference-DOI: 10.1038/EMBOJ.2012.204

(-) Compounds

Molecule 1 - PROTEIN ARGONAUTE 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MID DOMAIN, UNP RESIDUES 579-727
    Gene: AGO2, AT1G31280, T19E23.7T19E23_8
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 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  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:649 , HOH A:926 , HOH B:913BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWARETYR A:678 , LYS A:682 , THR A:693 , GLN A:694 , CYS A:695 , LYS A:719 , HOH A:953BINDING SITE FOR RESIDUE SO4 A 802
3AC3SOFTWAREHIS A:590 , HIS A:659 , HOH A:958 , TRP B:618 , GLN B:623BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWAREASN A:612 , ARG A:616 , ARG A:709 , HOH A:907 , HOH A:920 , HOH A:939 , LYS B:658BINDING SITE FOR RESIDUE SO4 A 804
5AC5SOFTWAREGLU A:654 , ARG A:657 , LYS A:658BINDING SITE FOR RESIDUE SO4 A 805
6AC6SOFTWAREGLU A:600 , ARG A:634 , MET A:635 , GLU A:636BINDING SITE FOR RESIDUE SO4 A 806
7AC7SOFTWAREILE A:587 , LYS A:589 , HIS A:590 , THR A:665BINDING SITE FOR RESIDUE SO4 A 807
8AC8SOFTWARETYR B:678 , LYS B:682 , THR B:693 , GLN B:694 , CYS B:695BINDING SITE FOR RESIDUE SO4 B 801
9AC9SOFTWAREASN B:612 , ARG B:616 , ARG B:709 , HOH B:909 , HOH B:936BINDING SITE FOR RESIDUE SO4 B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G0M)

(-) Exons   (0, 0)

(no "Exon" information available for 4G0M)

(-) 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:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeee............hhhhhhhhhhhhh..ee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhh...eeeeeehhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g0m A 586 SIVKHWAVLDFTASERFNKMPNDFVDNLIDRCWRLGMQMEAPIVYKTSRMETLSNGNAIEELLRSVIDEASRKHGGARPTLVLCAMSRKDDGYKTLKWIAETKLGLVTQCFLTGPATKGGDQYRANLALKMNAKV 720
                                   595       605       615       625       635       645       655       665       675       685       695       705       715     


Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee............hhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhh..eeeeeehhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g0m B 588 VKHWAVLDFTASERFNKMPNDFVDNLIDRCWRLGMQMEAPIVYKTSRMETLSNGNAIEELLRSVIDEASRKHGGARPTLVLCAMSRKDDGYKTLKWIAETKLGLVTQCFLTGPATKGGDQYRANLALKMNAK 719
                                   597       607       617       627       637       647       657       667       677       687       697       707       717
   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 4G0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G0M)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4g0o CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO5 MID DOMAIN
4g0p STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH UMP
4g0q STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH CMP
4g0x CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN
4g0y STRUCTURE OF ARABIDOPSIS AGO1 IN COMPLEX WITH AMP
4g0z STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH GMP