Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  HUMAN ALU RNA RETROTRANSPOSITION COMPLEX IN THE RIBOSOME-STALLING CONFORMATION
 
Authors :  V. Ahl, O. Weichenrieder
Date :  12 Sep 15  (Deposition) - 11 Nov 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Translation, Retrotransposition, Protein Targeting, Rna, Mobile Dna, Sine, Line, Ribonucleoprotein Particle, Signal Recognition Particle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Ahl, H. Keller, S. Schmidt, O. Weichenrieder
Retrotransposition And Crystal Structure Of An Alu Rnp In The Ribosome-Stalling Conformation.
Mol. Cell V. 60 715 2015
PubMed-ID: 26585389  |  Reference-DOI: 10.1016/J.MOLCEL.2015.10.003

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA II
    Fragment: UNP RESIDUES 2-86
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP9
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM41
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA II
    Fragment: UNP RESIDUES 2-95
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRP14,18 KDA ALU RNA-BINDING PROTEIN, SRP14
 
Molecule 3 - ALU JO CONSENSUS RNA
    Chains: C, F
    Fragment: ALU JO LEFT TRUNCATED MONOMER
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GDP2Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
3MG4Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GDP1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GDP1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:61 , HOH B:2027 , U C:24 , G C:25BINDING SITE FOR RESIDUE ACT C1001
2AC2SOFTWAREC C:3 , C C:4BINDING SITE FOR RESIDUE SO4 C1011
3AC3SOFTWARETYR B:33 , SER B:68 , VAL B:70 , HOH B:2048 , A C:27 , A C:28 , HOH C:2155 , HOH C:2156BINDING SITE FOR RESIDUE PEG C1051
4AC4SOFTWAREA C:57 , G C:59 , HOH C:2110 , HOH C:2111 , HOH C:2112 , HOH C:2113BINDING SITE FOR RESIDUE MG C1101
5AC5SOFTWAREU C:17 , G C:41 , HOH C:2046 , HOH C:2047 , HOH C:2086BINDING SITE FOR RESIDUE MG C1111
6AC6SOFTWAREC C:108 , HOH C:2011 , HOH C:2012 , HOH C:2015 , HOH C:2141 , HOH C:2142BINDING SITE FOR RESIDUE MG C1131
7AC7SOFTWARETHR E:61 , U F:24 , G F:25BINDING SITE FOR RESIDUE ACT F1001
8AC8SOFTWAREC F:3 , C F:4 , HOH F:2047BINDING SITE FOR RESIDUE SO4 F1011
9AC9SOFTWAREC F:108 , HOH F:2007 , HOH F:2010 , HOH F:2061 , HOH F:2062 , HOH F:2066BINDING SITE FOR RESIDUE MG F1131

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AOX)

(-) 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:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhh.....eeeeeee....eeeeeee....eeeeee...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5aox A   2 PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVSLVYKTDQAQDVKKIEKFHSQLMRLMVAKE  77
                                    11        21        31        41        51        61        71      


Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......eeeeeee..............eeeeeee....eeeeeee...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 5aox B   2 GAMESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIFEPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
                                    11        21        31        49        59        69        79        89      
                                                                 40|                                              
                                                                  49                                              


Chain C from PDB  Type:DNA/RNA  Length:87
                                                                                                                       
                 5aox C   1 xGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGAGGAUCGCGAACACGCGAGACCCCGUCUCUA 118
                            |       10        20        30        40        50        60       101       111       
                            1-GDP                                                              69|                 
                                                                                               101                 


Chain D from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.......eeeeeee....eeeeeee....eeeeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5aox D   2 PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVSLVYKTDQAQDVKKIEKFHSQLMRLMV  74
                                    11        21        31        41        51        61        71   


Chain E from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......eeeeeeee...........eeeeeee....eeeeeeehhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 5aox E   2 GAMESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
                                    11        21        31        51        61        71        81        91    
                                                                 40|                                            
                                                                  51                                            


Chain F from PDB  Type:DNA/RNA  Length:87
                                                                                                                       
                 5aox F   1 xGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGAGGAUCGCGAACACGCGAGACCCCGUCUCUA 118
                            |       10        20        30        40        50        60       101       111       
                            1-GDP                                                              69|                 
                                                                                               101
   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 5AOX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 29)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5aox)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5aox
    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
  SRP09_HUMAN | P49458
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SRP14_HUMAN | P37108
    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
  SRP09_HUMAN | P49458
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SRP14_HUMAN | P37108
    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
        SRP09_HUMAN | P49458: 1e8o 1e8s 1ry1 4uyj 4uyk
        SRP14_HUMAN | P37108: 1e8o 1e8s 1ry1 4uyj 4uyk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AOX)