Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE SCHIZOSACCHAROMYCES POMBE MEDIATOR HEAD MODULE
 
Authors :  L. Lariviere, C. Plaschka, M. Seizl, L. Wenzeck, F. Kurth, P. Cramer
Date :  19 Sep 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  F,H,K,Q,R,V
Keywords :  Transcription, Mediator Complex, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lariviere, C. Plaschka, M. Seizl, L. Wenzeck, F. Kurth, P. Cramer
Structure Of The Mediator Head Module.
Nature V. 492 448 2012
PubMed-ID: 23123849  |  Reference-DOI: 10.1038/NATURE11670

(-) Compounds

Molecule 1 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 6
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED6, PMC5, SPAC1002.15C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: MEDIATOR COMPLEX SUBUNIT 6, RNA POLYMERASE II MEDIATOR COMPLEX PROTEIN PMC5
 
Molecule 2 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 8
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED8, SEP15, SPBC21.04
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: CELL SEPARATION PROTEIN SEP15, MEDIATOR COMPLEX SUBUNIT 8
 
Molecule 3 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 11
    Chains: K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED11, SPAC644.10
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: MEDIATOR COMPLEX SUBUNIT 11
 
Molecule 4 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 17
    Chains: Q
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED17, SPBC31F10.04C, SRB4
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: MEDIATOR COMPLEX SUBUNIT 17, SUPPRESSOR OF RNA POLYMERASE B 4 HOMOLOG
 
Molecule 5 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 18
    Chains: R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED18, PMC6, SEP11, SPAC5D6.05
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: CELL SEPARATION PROTEIN SEP11, MEDIATOR COMPLEX SUBUNIT 18, RNA POLYMERASE II MEDIATOR COMPLEX PROTEIN PMC6
 
Molecule 6 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 22
    Chains: V
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MED22, SPAC29A4.07, SRB6
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: 972H
    Synonym: MEDIATOR COMPLEX SUBUNIT 22, SUPPRESSOR OF RNA POLYMERASE B 6 HOMOLOG

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : FHKQRV

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4H63)

(-) Sites  (0, 0)

(no "Site" information available for 4H63)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H63)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro F:85 -Pro F:86
2Pro Q:161 -Pro Q:162
3Gly R:28 -Pro R:29
4Pro R:154 -Pro R:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H63)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H63)

(-) Exons   (0, 0)

(no "Exon" information available for 4H63)

(-) 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 F from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhhhh.......hhhhhhh........hhhhhh..hhhhhh.eeeeeeeeee...eeeeeeeee.....eeeeeeeeee..eee...hhhhhhhhhhhhhhhhhhhhhhhhh...eee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h63 F  10 DLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLLNSQLKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNATYCFQKALTKIEKFPQYNPQEGYTYP 158
                                    19        29        39        49  ||    72        82        92       102       112       122       132       142       152      
                                                                     52|                                                                                            
                                                                      66                                                                                            


Chain H from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee........hhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h63 H   3 DISTEKTVESLEAIRHRIAQIVQSLTHFLAILHQSESLSPWPTIHKNFNILLSQIHSLSNNLAAHSHTLQTTSIYPSLEFPVKEQEPLLTTLLRTKALPEVEEWEANTLQEYEASIANDAYQKDQLWDQARIIFMEERENYSWFRQLEIDRATEEQNANQMLTDILSFMKSGKR 200
                                    12        22        32        42        52        62        72        82        92       102       112     ||130       140       150   ||  176       186       196    
                                                                                                                                             118|                        154|                             
                                                                                                                                              127                         171                             


Chain K from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4h63 K  15 SSDTQQVQNILELEAKIPDILSSAGKCIEAIQLNNSLEDFRKYSKEFLETVEFISTGLRRQALELEKAEVPVVSLQPKKRYASTPLSNLIFDQSSKLM 112
                                    24        34        44        54        64        74        84        94       104        


Chain Q from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee......eee............eeeee......eeee........eeeeeee.....eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...eeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhh..hhhhhhhhh.....eeeeeee.......eeeee.......eeee....eeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h63 Q  99 MDSQAYKKELIEQIMIAQTECSLALDMTSLLLSKFKENSIETISPFLKSTVPPSSLQFSRSQPPESKESDATLAKCWKEKSLTSSCKFLFEAKERLTSVVETEHEYYTELVKVKEASWPLFNSQGSNHLSVQYSCLGGISLGLGLIRMKPESKSFEVQSSLLYSQAALKISILNKDRDEIGSSTWSWPSQNCNSVLLKDIYKLQEILFEMDIWNSLLQEAQSCGNQGVNFTGDEILVPISDDHVVRITLETSSTNFVTIKQEKELLKCLCDTLNAIAHILFLKHCRKSDRRSQQDANAPLILRPLIFYYNLNQESLEFQRWLKQRDISFKFMPNYPWEKAKDFLELENSLSINRLSISWRIMVSNFEPAIFIQHTPTLHGVWRCKDQYSSNQFSSLKNVCQYIEHHINSL 537
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348 ||    376       386       396       406   ||  423       433       443       453       463       473       483       493       503|      517       527       537
                                                                                                                                                                                                                                                                                     350|                                      410|                                                                                  503|                             
                                                                                                                                                                                                                                                                                      369                                       418                                                                                   508                             


Chain R from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhh..eeeeeeeeeeeeeee........eeeeee................eeeeee...........eeeeeeeeee.............eeeeeeeeeeeeeeee..eeeeeeeeee...........ee......eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h63 R   1 MQELYLLGVVPSRRFEAVVNSLSKTLDGPKTILEFWVVYRPKPRQPDSWLRLCSNIESHDETDTEWSKNTQWSMYLEGNSEPKREDKCGIRPVNRAKLTNGSVTEFVEKMGYEFSHEYIIQGLEYFFFDTTVRIYQTLIPSQQRSIKPPFHPMNEEQPWILHVYTHVADASNQVAMAKAEANLTKVKTLLSAFCDLKNVRL 207
                                    10        20        30        40 ||     56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206 
                                                                    42|                                                                                                                                                              
                                                                     49                                                                                                                                                              


Chain V from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4h63 V   5 SFQRQLVQRTNTLNSSIDNATLTILSRFQDILDIAINEGKDKYTVAPEVYQIECHTVSMVRAVEQLLDVSRQIKSYWLTNSLSTSFPTVDYSEPDLEKVKRTLTKLQNHLLEVSLIE 121
                                    14        24        34        44        54        64        74        84        94       104       114
   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 4H63)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H63)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H63)

(-) Gene Ontology  (15, 52)

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
(no "Ligands, Modified Residues, Ions" information available for 4h63)
 
  Sites
(no "Sites" information available for 4h63)
 
  Cis Peptide Bonds
    Gly R:28 - Pro R:29   [ RasMol ]  
    Pro F:85 - Pro F:86   [ RasMol ]  
    Pro Q:161 - Pro Q:162   [ RasMol ]  
    Pro R:154 - Pro R:155   [ 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 ](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
  4h63
    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
  MED11_SCHPO | Q9P6Q0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MED17_SCHPO | P87306
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MED18_SCHPO | O14198
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MED22_SCHPO | O14010
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MED6_SCHPO | Q9US45
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MED8_SCHPO | O94646
    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
  MED11_SCHPO | Q9P6Q0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MED17_SCHPO | P87306
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MED18_SCHPO | O14198
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MED22_SCHPO | O14010
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MED6_SCHPO | Q9US45
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MED8_SCHPO | O94646
    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
        MED11_SCHPO | Q9P6Q0: 5n9j 5u0p 5u0s
        MED17_SCHPO | P87306: 5n9j 5u0p 5u0s
        MED18_SCHPO | O14198: 3c0t 5n9j 5u0p 5u0s
        MED22_SCHPO | O14010: 5n9j 5u0p 5u0s
        MED6_SCHPO | Q9US45: 4h61 5n9j 5u0p 5u0s
        MED8_SCHPO | O94646: 3c0t 5n9j 5u0p 5u0s

(-) Related Entries Specified in the PDB File

4h61 4h62