Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN
 
Authors :  F. Frank, J. Hauver, N. Sonenberg, B. Nagar
Date :  10 Jul 12  (Deposition) - 25 Jul 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
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 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Fragment: MID DOMAIN, UNP RESIDUES 593-738
    Gene: AGO1, AT1G48410, F11A17.3, T1N15.2
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:98 , LYS A:102 , SER A:113 , GLN A:114 , CYS A:115 , LYS A:135 , LYS A:139 , SO4 A:202BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARELYS A:102 , GLU A:106 , VAL A:112 , SER A:113 , LYS A:139 , LEU A:147 , SO4 A:201 , HOH A:354 , HOH A:400BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARESER A:20 , ARG A:21 , GLN A:22 , PRO A:91 , HOH A:320 , HOH A:327 , HOH A:352 , HOH A:363 , HOH A:413 , HOH A:449BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREARG A:21 , ARG A:58 , PRO A:59 , GLU A:60 , HOH A:366 , HOH A:422BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWAREHIS A:120 , LYS A:123 , SER A:125 , HOH A:309 , HOH A:368 , HOH A:427 , HOH A:430BINDING SITE FOR RESIDUE SO4 A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G0X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G0X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G0X)

(-) Exons   (0, 0)

(no "Exon" information available for 4G0X)

(-) 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:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..ee..eeeee.....hhhhhhhhhhhhhhhhhhh..ee........ee.hhhhhhhhhhhhhhhhhhh........eeeeee.....hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g0x A   1 SNKKmINGGTVNNWICINFSRQVQDNLARTFCQELAQmCYVSGmAFNPEPVLPPVSARPEQVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKHVFKmSKQYmANVALKINVKVGGRNTVL 147
                                |   10        20        30       |40   |    50        60        70        80        90       100       110       120   |   130       140       
                                |                               38-MSE |                                                                             124-MSE|                  
                                5-MSE                                 44-MSE                                                                              129-MSE
   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 4G0X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G0X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G0X)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4g0x)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4g0x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AGO1_ARATH | O04379
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AGO1_ARATH | O04379
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AGO1_ARATH | O04379: 3vna 3vnb 4g0p 4g0q 4g0y 4g0z

(-) Related Entries Specified in the PDB File

4g0m CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGO2 MID DOMAIN
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
4g0y STRUCTURE OF ARABIDOPSIS AGO1 IN COMPLEX WITH AMP
4g0z STRUCTURE OF ARABIDOPSIS THALIANA AGO1 MID DOMAIN IN COMPLEX WITH GMP