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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  X-RAY ANALYSIS OF A RNA TETRAPLEX R(UGGGGU)4 AT ULTRA-HIGH RESOLUTION
 
Authors :  J. Deng, Y. Xiong, M. Sundaralingam
Date :  21 May 01  (Deposition) - 23 Nov 01  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.61
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Biol. Unit 3:  C  (4x)
Biol. Unit 4:  D  (4x)
Keywords :  Rna Tetraplex, Sr Ions, U Tetrad, Octaplex, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Deng, Y. Xiong, M. Sundaralingam
X-Ray Analysis Of An Rna Tetraplex (Uggggu)(4) With Divalen Sr(2+) Ions At Subatomic Resolution (0. 61 A).
Proc. Natl. Acad. Sci. Usa V. 98 13665 2001
PubMed-ID: 11707581  |  Reference-DOI: 10.1073/PNAS.241374798

(-) Compounds

Molecule 1 - 5'-R(*UP*GP*GP*GP*GP*U)-3'
    ChainsA, B, C, D
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (4x)A   
Biological Unit 2 (4x) B  
Biological Unit 3 (4x)  C 
Biological Unit 4 (4x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2NA2Ligand/IonSODIUM ION
3SPM1Ligand/IonSPERMINE
4SR8Ligand/IonSTRONTIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SPM4Ligand/IonSPERMINE
4SR-1Ligand/IonSTRONTIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SPM-1Ligand/IonSPERMINE
4SR-1Ligand/IonSTRONTIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SPM-1Ligand/IonSPERMINE
4SR-1Ligand/IonSTRONTIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SPM-1Ligand/IonSPERMINE
4SR-1Ligand/IonSTRONTIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:2 , G A:3 , HOH A:67 , HOH A:137 , HOH A:151 , HOH A:164 , G B:14 , G B:15 , HOH B:109 , HOH B:177 , U C:21 , G C:22 , HOH C:184BINDING SITE FOR RESIDUE SPM A 62
02AC2SOFTWAREG D:34 , G D:35BINDING SITE FOR RESIDUE SR D 501
03AC3SOFTWAREG B:12 , G B:13BINDING SITE FOR RESIDUE SR B 502
04AC4SOFTWAREG C:22 , G C:23BINDING SITE FOR RESIDUE SR C 503
05AC5SOFTWAREG C:24 , G C:25 , HOH C:102BINDING SITE FOR RESIDUE SR C 504
06AC6SOFTWAREG A:4 , G A:5 , NA A:512BINDING SITE FOR RESIDUE SR A 505
07AC7SOFTWAREG A:2 , G A:3BINDING SITE FOR RESIDUE SR A 506
08AC8SOFTWAREG B:14 , G B:15BINDING SITE FOR RESIDUE SR B 507
09AC9SOFTWAREG D:32 , G D:33BINDING SITE FOR RESIDUE SR D 508
10BC1SOFTWAREU C:26 , HOH C:121 , HOH C:125 , HOH C:127 , HOH C:198 , HOH C:199 , HOH C:200BINDING SITE FOR RESIDUE CA C 509
11BC2SOFTWAREU A:1 , HOH A:118 , HOH A:146 , HOH A:149 , HOH A:156 , G B:13 , HOH C:122 , HOH C:205BINDING SITE FOR RESIDUE CA B 510
12BC3SOFTWAREU A:6 , HOH A:157 , HOH A:185 , HOH A:187 , HOH A:191 , HOH A:201 , HOH A:206BINDING SITE FOR RESIDUE CA A 511
13BC4SOFTWAREG A:5 , U A:6 , SR A:505BINDING SITE FOR RESIDUE NA A 512
14BC5SOFTWAREG B:15 , U B:16 , HOH B:101BINDING SITE FOR RESIDUE NA B 513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J8G)

(-) Exons   (0, 0)

(no "Exon" information available for 1J8G)

(-) 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:RNA  Length:6
                                     
                  1j8g A  1 UGGGGU  6

Chain B from PDB  Type:RNA  Length:6
                                     
                  1j8g B 11 UGGGGU 16

Chain C from PDB  Type:RNA  Length:6
                                     
                  1j8g C 21 UGGGGU 26

Chain D from PDB  Type:RNA  Length:6
                                     
                  1j8g D 31 UGGGGU 36

   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 1J8G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1J8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J8G)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1J8G)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SR  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1j8g)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1j8g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP | HSSP
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1J8G)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1J8G)