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 :  STRUCTURAL BASIS FOR THE ACTIVITY OF A CYTOPLASMIC RNA TERMINAL U-TRANSFERASE
 
Authors :  L. A. Yates, S. Fleurdepine, O. S. Rissland, L. Decolibus, K. Harlos, C. J. Norbury, R. J. C. Gilbert
Date :  19 Mar 12  (Deposition) - 04 Jul 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Polymerase-Like Nucleotidyl Transferase, Terminal Uridine Transferase, Utp, Rna, Cytoplasmic, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Yates, S. Fleurdepine, O. S. Rissland, L. De Colibus, K. Harlos, C. J. Norbury, R. J. Gilbert
Structural Basis For The Activity Of A Cytoplasmic Rna Terminal Uridylyl Transferase.
Nat. Struct. Mol. Biol. V. 19 782 2012
PubMed-ID: 22751018  |  Reference-DOI: 10.1038/NSMB.2329

(-) Compounds

Molecule 1 - POLY(A) RNA POLYMERASE PROTEIN CID1
    Chains: A, B, C, D
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: CID1, SPAC19D5.03
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE 972H-
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: CAFFEINE-INDUCED DEATH PROTEIN 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1UTP4Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:88 , GLY A:89 , SER A:90 , SER A:100 , ALA A:168 , ASN A:171 , THR A:172 , LYS A:193 , LYS A:197 , SER A:211 , TYR A:212 , HIS A:336BINDING SITE FOR RESIDUE UTP A 501
2AC2SOFTWAREPHE B:88 , GLY B:89 , SER B:90 , SER B:100 , ALA B:168 , ASN B:171 , THR B:172 , LYS B:193 , LYS B:197 , SER B:211 , TYR B:212 , HIS B:336 , HOH B:601BINDING SITE FOR RESIDUE UTP B 501
3AC3SOFTWAREPHE C:88 , GLY C:89 , SER C:90 , SER C:100 , ALA C:168 , ASN C:171 , THR C:172 , LYS C:193 , LYS C:197 , SER C:211 , TYR C:212 , HIS C:336 , HOH C:601BINDING SITE FOR RESIDUE UTP C 501
4AC4SOFTWAREGLY D:89 , SER D:90 , ALA D:168 , ASN D:171 , THR D:172 , LYS D:193 , LYS D:197 , SER D:211 , TYR D:212 , HIS D:336 , HOH D:601BINDING SITE FOR RESIDUE UTP D 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E80)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Lys A:227 -Pro A:228
2Tyr A:366 -Pro A:367
3Lys B:227 -Pro B:228
4Tyr B:366 -Pro B:367
5Lys C:227 -Pro C:228
6Tyr C:366 -Pro C:367
7Lys D:227 -Pro D:228
8Tyr D:366 -Pro D:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E80)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E80)

(-) Exons   (0, 0)

(no "Exon" information available for 4E80)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhhh.eeeeeee..eeeeeeee......eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh.........................hhhhhhhhhhhhhhhhhhhh......hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e80 A   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPI  379
                                    50        60        70        80        90       100       115       125       135       145  ||   160       170       180       190       200      |210       220       230       240       250       260       270       280       290       300       322       332       342       352       362       372       
                                                                                              109|                              148|                                                 207A                                                                                                  308|                                                          
                                                                                               115                               154                                                                                                                                                        321                                                          


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhhh..eeeeee..eeeeee....eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh.......................hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e80 B   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPI  379
                                    50        60        70        80        90       100       115       125       135       145 ||    164       174       184       194       204  |    214       224       234       244       254       264       274       284       294       304   ||  328       338       348       358       368       378 
                                                                                              109|                             147|                                              207A                                                                                                  308|                                                        
                                                                                               115                              157                                                                                                                                                     323                                                        


Chain C from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh.......eeeeee......hhhhhhhhhhhhhh.eeeeeee..eeeeeeee...eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh.......hhhhh......ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh.................hhhhhh....eeee.....eeee....................hhhhhhhhhhhhhhhhhhhh......hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e80 C   42 KEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIPP  381
                                    51        61        71        81        91       101       111|      123       133       143    || 161       171       181       191       201     | 211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
                                                                                               111|                               148|                                              207A                                                                                                                                                                              
                                                                                                114                                157                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......eeeeee...hhhhhhhhhhhhhh.eeeeeee..eeeeeeee...eeeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh..................ee..ee.....hhhhh.......hhhhhhhhhhhhhhhh......ee.........hhhhhh..................ee..............hhhhhhhhhhhhhhhhhhhh......hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4e80 D   41 HKEFTKFCYEVYNEIKISDKEFKEKRAALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSSFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNSRSYPIPYDSLFEEAPIP  380
                                    50        60        70        80        90       100       115       125       135       145 ||    163       173       183       193       203   |   213       223       233       243       253       263       273       283       293       303       313   ||  326       336       346       356       366       376    
                                                                                              109|                             147|                                               207A                                                                                                           317|                                                           
                                                                                               115                              156                                                                                                                                                               321
   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 4E80)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E80)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E80)

(-) 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
    UTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:227 - Pro A:228   [ RasMol ]  
    Lys B:227 - Pro B:228   [ RasMol ]  
    Lys C:227 - Pro C:228   [ RasMol ]  
    Lys D:227 - Pro D:228   [ RasMol ]  
    Tyr A:366 - Pro A:367   [ RasMol ]  
    Tyr B:366 - Pro B:367   [ RasMol ]  
    Tyr C:366 - Pro C:367   [ RasMol ]  
    Tyr D:366 - Pro D:367   [ RasMol ]  
 
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
[ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4e80
    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 4e8f 4ep7 4fh3 4fh5 4fhp 4fhv 4fhw 4fhx 4fhy 4nkt 4nku 4ud4 4ud5

(-) Related Entries Specified in the PDB File

4e7x APO STRUCTURE, FORM I
4e8f ACETATE BOUND FORM