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
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)

(-) Description

Title :  NOVEL MODIFICATIONS ON C-TERMINAL DOMAIN OF RNA POLYMERASE II CAN FINE-TUNE THE PHOSPHATASE ACTIVITY OF SSU72
 
Authors :  Y. Luo, S. D. Yogesha, Y. Zhang
Date :  03 Jan 13  (Deposition) - 07 Aug 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym. Unit :  A,B,C,D,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Ssu72, Symplekin, Ctd, Ctd Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Luo, S. D. Yogesha, J. R. Cannon, W. Yan, A. D. Ellington, J. S. Brodbelt, Y. Zhang
Novel Modifications On C-Terminal Domain Of Rna Polymerase Ii Can Fine-Tune The Phosphatase Activity Of Ssu72.
Acs Chem. Biol. V. 8 2042 2013
PubMed-ID: 23844594  |  Reference-DOI: 10.1021/CB400229C

(-) Compounds

Molecule 1 - SYMPLEKIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B DERIVATIVE PLASMID
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SYM, CG2097, DMEL_CG2097
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: LD45768P
 
Molecule 2 - CG14216
    Chains: B, D
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B DERIVATIVE PLASMID
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SSU72, CG14216, DMEL_CG14216
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: LD40846P
 
Molecule 3 - CTD
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN EUKARYOTES.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDF
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   CDF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2SEP-1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
2SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:13 , SER B:14 , SER B:15 , ASN B:16 , MET B:17 , ASN B:18 , ARG B:19 , ASN B:144BINDING SITE FOR RESIDUE PO4 B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Sep F:5 -Pro F:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMJ)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imj A  18 MTDEKTATARAKVVDWCNELVIASPSTKCELLAKVQETVLGSCAELAEEFLESVLSLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYKNGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFADEDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLCTIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTIRGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAA 350
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347   


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh...eeeeee....eee......eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....eeee.hhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imj B   4 PSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    13        23        33        43  ||    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
                                                                     46|                                                                                                                                                  
                                                                      49                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imj C  42 PSTKCELLAKVQETVLGSCAELAEEFLESVLSLAHDSNMEVRKQVVAFVEQVCKVKVELLPHVINVVSMLLRDNSAQVIKRVIQACGSIYKNGLQYLCSLMEPGDSAEQAWNILSLIKAQILDMIDNENDGIRTNAIKFLEGVVVLQSFADEDSLKRDGDFSLADVPDHCTLFRREKLQEEGNNILDILLQFHGTTHISSVNLIACTSSLCTIAKMRPIFMGAVVEAFKQLNANLPPTLTDSQVSSVRKSLKMQLQTLLKNRGAFEFASTIRGMLVDLGSSTNEIQKLIPKMDKQEMARRQKRILENAA 350
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         


Chain D from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh...eeeeee....eeeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....eeee.hhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4imj D   4 PSKLAVAVVDSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPGMAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHMLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVMHMESMESVDNRPVHVLNVDVVNNAEDALMGAFVITDMINMMAKSTDLDNDIDELIQEFEERRKRVILHSVLFY 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  


Chain F from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4imj F   2 SPTsPSYS   9
                               |    
                               5-SEP
   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 4IMJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 18)

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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Sep F:5 - Pro F:6   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4imj
    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
  Q9VWE4_DROME | Q9VWE4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  SYMPK_DROME | Q8MSU4
    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)
  3.1.3.16
    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
  Q9VWE4_DROME | Q9VWE4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SYMPK_DROME | Q8MSU4
    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
        SYMPK_DROME | Q8MSU4: 3gs3 4imi 4ygx
UniProtKB/TrEMBL
        Q9VWE4_DROME | Q9VWE4: 3fdf 3fmv 3omw 3omx 3p9y 4imi 4ygx

(-) Related Entries Specified in the PDB File

4imi