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

(-) Description

Title :  STRUCTURAL PLASTICITY OF CID1 PROVIDES A BASIS FOR ITS RNA TERMINAL URIDYLYL TRANSFERASE ACTIVITY
 
Authors :  L. A. Yates, B. P. Durrant, S. Fleurdepine, K. Harlos, C. J. Norbury, R. J. C. Gilbert
Date :  07 Dec 14  (Deposition) - 18 Mar 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Caffeine, Uridylyltransferase Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Yates, B. P. Durrant, S. Fleurdepine, K. Harlos, C. J. Norbury, R. J. C. Gilbert
Structural Plasticity Of Cid1 Provides A Basis For Its Distributive Rna Terminal Uridylyl Transferase Activity.
Nucleic Acids Res. V. 43 2968 2015
PubMed-ID: 25712096  |  Reference-DOI: 10.1093/NAR/GKV122

(-) Compounds

Molecule 1 - POLY(A) RNA POLYMERASE PROTEIN CID1
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-TCID1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: CAFFEINE-INDUCED DEATH PROTEIN 1, CAFFEINE-INDUCED DEATH SUPPRESSOR 1 URIDYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4UD5)

(-) Sites  (0, 0)

(no "Site" information available for 4UD5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UD5)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:227 -Pro A:228
2Tyr A:366 -Pro A:367
3Gly B:154 -Ala B:155
4Lys B:227 -Pro B:228
5Tyr B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UD5)

(-) Exons   (0, 0)

(no "Exon" information available for 4UD5)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee.....hhhhhhhhhhhhh.eeeeeeee..eeeeeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhh..................hhhhhh....eeee.....eeee....................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ud5 A   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSSDTIALQFYEELIAEGFEGAFLQAARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFAFYAYAFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIPP  381
                                    50        60        70        80        90       100       110|      123       133       143       153       163       173       183       193       203   |   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373        
                                                                                               110|                                                                                         207A                                                                                                                                                                              
                                                                                                114                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeee..........eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhh..................hhhhhh....eeee.....eeee....................hhhhhhhhhhhhhhhhhhhhh.....hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ud5 B   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGAFLQAARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFAFYAYAFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIPPR  382
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  
                                                                                                                                                                                               207A
   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 4UD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UD5)

(-) Gene Ontology  (14, 14)

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
(no "Ligands, Modified Residues, Ions" information available for 4ud5)
 
  Sites
(no "Sites" information available for 4ud5)
 
  Cis Peptide Bonds
    Gly B:154 - Ala B:155   [ RasMol ]  
    Lys A:227 - Pro A:228   [ RasMol ]  
    Lys B:227 - Pro B:228   [ RasMol ]  
    Tyr A:366 - Pro A:367   [ RasMol ]  
    Tyr B:366 - Pro B:367   [ RasMol ]  
 
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 | Biol. Unit 1 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
  4ud5
    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
  CID1_SCHPO | O13833
    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)
  2.7.7.-
    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
  CID1_SCHPO | O13833
    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
        CID1_SCHPO | O13833: 4e7x 4e80 4e8f 4ep7 4fh3 4fh5 4fhp 4fhv 4fhw 4fhx 4fhy 4nkt 4nku 4ud4

(-) Related Entries Specified in the PDB File

4ud4 STRUCTURAL PLASTICITY OF CID1 PROVIDES A BASIS FOR ITS RNA TERMINAL URIDYLYL TRANSFERASE ACTIVITY