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 :  STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN-HYDROLASE-RNASE MODULE
 
Authors :  I. B. Schaefer, E. Conti
Date :  27 Apr 14  (Deposition) - 04 Jun 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin Carboxyl-Terminal Hydrolase-Like Domain, Uch, Rnase, Pan3, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. B. Schafer, M. Rode, F. Bonneau, S. Schussler, E. Conti
The Structure Of The Pan2-Pan3 Core Complex Reveals Cross-Talk Between Deadenylase And Pseudokinase.
Nat. Struct. Mol. Biol. V. 21 591 2014
PubMed-ID: 24880344  |  Reference-DOI: 10.1038/NSMB.2834

(-) Compounds

Molecule 1 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
    Chains: A
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFL
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 460-1115
    Gene: PAN2, YGL094C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:910 , GLU A:912 , ASP A:1071 , MG A:1202BINDING SITE FOR RESIDUE MG A 1201
2AC2SOFTWAREASP A:910 , GLU A:912 , HIS A:1066 , ASP A:1071 , MG A:1201BINDING SITE FOR RESIDUE MG A 1202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q8H)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Phe A:489 -Gly A:490
2Gly A:490 -Thr A:491
3Thr A:491 -Asp A:492
4Arg A:616 -Asn A:617
5Ser A:676 -Gly A:677
6Ala A:881 -Asn A:882
7Lys A:935 -Arg A:936
8Leu A:979 -Pro A:980
9Arg A:995 -Asn A:996
10Ile A:1033 -Arg A:1034
11Glu A:1063 -Gly A:1064
12Asn A:1065 -His A:1066

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q8H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q8H)

(-) 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:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh..................................hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhh...............hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.eeeeeeeeee..eeeeeeeee..eee.........hhhhhhhhheeeeee............eeeeeee.....eeeeee..hhhhhhhhhhh......eeeeeee..eeeee............eeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeee..eeeeehhhhhhh.....eeeeeeeeeehhhhh....hhhhh...hhhhhh..................hhhhh.....eeeeeeeeee...............eeeeeeeeee.........eeeeeee.........hhhhhh.............ee...hhhhhhhhhhhhhh.eee..hhhhhhhhhh...hhhhh.hhhhhh.......hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q8h A  459 PETSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQEEYLESLCIRESIEDFNSSESIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINKTGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFFSVDTYSINYDILFRDYFANGIRDTARREYKLLTHDEAPKSGTLVAIDAEFVSLQSELCEIDHIRPKRTALARISIIRGEEGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTAIYFLQGKRYLSLRYLAYVLLGMNIQEGNHDSIEDAHTALILYKKYLHLKEKAIFEKVLNSVYEEGRAHNFKVPE 1111
                                   468       478       488       498       508       518       528       538       548       558       568       578   ||  598       608       618       628       638       648       658       668       678  ||   698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918      |934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104       
                                                                                                                                                     582|                                                                                     681|                                                                                                                                                                                                                                      925|                                                                                                                                                                                   
                                                                                                                                                      593                                                                                      692                                                                                                                                                                                                                                       932
   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 4Q8H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q8H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q8H)

(-) Gene Ontology  (15, 15)

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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:881 - Asn A:882   [ RasMol ]  
    Arg A:616 - Asn A:617   [ RasMol ]  
    Arg A:995 - Asn A:996   [ RasMol ]  
    Asn A:1065 - His A:1066   [ RasMol ]  
    Glu A:1063 - Gly A:1064   [ RasMol ]  
    Gly A:490 - Thr A:491   [ RasMol ]  
    Ile A:1033 - Arg A:1034   [ RasMol ]  
    Leu A:979 - Pro A:980   [ RasMol ]  
    Lys A:935 - Arg A:936   [ RasMol ]  
    Phe A:489 - Gly A:490   [ RasMol ]  
    Ser A:676 - Gly A:677   [ RasMol ]  
    Thr A:491 - Asp A:492   [ RasMol ]  
 

(-) 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
  4q8h
    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
  PAN2_YEAST | P53010
    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)
  3.1.13.4
    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
  PAN2_YEAST | P53010
    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
        PAN2_YEAST | P53010: 4q8g 4xr7

(-) Related Entries Specified in the PDB File

4q8g STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN-HYDROLASE
4q8j STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2-PAN3 CORE COMPLEX