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 :  NAB2 ZN FINGERS 5-7 BOUND TO A11G RNA
 
Authors :  M. Stewart, S. Aibara
Date :  02 Aug 16  (Deposition) - 21 Dec 16  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Nab2, Zn Finger, Rna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Aibara, J. M. Gordon, A. S. Riesterer, S. H. Mclaughlin, M. Stewart
Structural Basis For The Dimerization Of Nab2 Generated By Rna Binding Provides Insight Into Its Contribution To Both Poly(A) Tail Length Determination And Transcript Compaction In Saccharomyces Cerevisiae.
Nucleic Acids Res. V. 45 1529 2017
PubMed-ID: 28180315  |  Reference-DOI: 10.1093/NAR/GKW1224

(-) Compounds

Molecule 1 - NAB2P
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAB2, H834_YJM1574G00138
    Organism Scientific: SACCHAROMYCES CEREVISIAE YJM1574
    Organism Taxid: 1294386
 
Molecule 2 - RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3')
    Chains: C, D, G, H
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1ZN14Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:415 , CYS A:421 , CYS A:426 , HIS A:430binding site for residue ZN A 501
02AC2SOFTWARECYS A:437 , CYS A:443 , CYS A:448 , HIS A:452binding site for residue ZN A 502
03AC3SOFTWARECYS A:458 , CYS A:464 , CYS A:469 , HIS A:473binding site for residue ZN A 503
04AC4SOFTWAREGLU A:413 , HOH A:614 , HOH A:621 , HOH A:680 , A G:3 , HOH G:138binding site for residue ZN A 504
05AC5SOFTWARECYS B:415 , CYS B:421 , CYS B:426 , HIS B:430binding site for residue ZN B 501
06AC6SOFTWARECYS B:437 , CYS B:443 , CYS B:448 , HIS B:452binding site for residue ZN B 502
07AC7SOFTWARECYS B:458 , CYS B:464 , CYS B:469 , HIS B:473binding site for residue ZN B 503
08AC8SOFTWARECYS E:415 , CYS E:421 , CYS E:426 , HIS E:430binding site for residue ZN E 501
09AC9SOFTWARECYS E:437 , CYS E:443 , CYS E:448 , HIS E:452binding site for residue ZN E 502
10AD1SOFTWARECYS E:458 , CYS E:464 , CYS E:469 , HIS E:473binding site for residue ZN E 503
11AD2SOFTWARECYS F:415 , CYS F:421 , CYS F:426 , HIS F:430binding site for residue ZN F 501
12AD3SOFTWARECYS F:437 , CYS F:443 , CYS F:448 , HIS F:452binding site for residue ZN F 502
13AD4SOFTWARECYS F:458 , CYS F:464 , CYS F:469 , HIS F:473binding site for residue ZN F 503
14AD5SOFTWAREGLY F:407 , HOH F:670 , HOH F:693binding site for residue ZN F 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L2L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L2L)

(-) Exons   (0, 0)

(no "Exon" information available for 5L2L)

(-) 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:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh.................hhhhh................hhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5l2l A 408 SEKSLEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDCLFGHPINEDCRFGVNCKNIYCLFRHPPGRVL 479
                                   417       427       437       447       457       467       477  


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.................hhhhh................hhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5l2l B 407 GSEKSLEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDCLFGHPINEDCRFGVNCKNIYCLFRHPPGRVLP 480
                                   416       426       436       446       456       466       476    


Chain C from PDB  Type:RNA  Length:10
                                          
                 5l2l C   3 AAAAAAAAAG  12
                                    12


Chain D from PDB  Type:RNA  Length:11
                                           
                 5l2l D   2 AAAAAAAAAAG  12
                                    11 


Chain E from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh.................hhhhh................hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5l2l E 409 EKSLEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDCLFGHPINEDCRFGVNCKNIYCLFRHPPGRVLP 480
                                   418       428       438       448       458       468       478  


Chain F from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.................hhhhh................hhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 5l2l F 407 GSEKSLEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDCLFGHPINEDCRFGVNCKNIYCLFRHPPGRVLPE 481
                                   416       426       436       446       456       466       476     


Chain G from PDB  Type:RNA  Length:10
                                          
                 5l2l G   3 AAAAAAAAAG  12
                                    12


Chain H from PDB  Type:RNA  Length:10
                                          
                 5l2l H   3 AAAAAAAAAG  12
                                    12
   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 5L2L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L2L)

(-) Gene Ontology  (16, 16)

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
    ZN  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l2l)
 

(-) 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
  5l2l
    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
  NAB2_YEAST | P32505
    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
  NAB2_YEAST | P32505
    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
        NAB2_YEAST | P32505: 2jps 2lhn 2v75 3lcn 3zj1 3zj2 4jlq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L2L)