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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CDK8-CYCLIN C IN COMPLEX WITH CORTISTATIN A
 
Authors :  A. G. Myers, M. D. Shair
Date :  27 Feb 14  (Deposition) - 23 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Cyclin-Dependent Kinase 8, Cdk8, Cyclin C, Ccnc, Cortistatin A, Mediator Kinase, Mediator Complex, Super-Enhancer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. E. Pelish, B. B. Liau, I. I. Nitulescu, A. Tangpeerachaikul, Z. C. Poss, D. H. Da Silva, B. T. Caruso, A. Arefolov, O. Fadeyi, A. L. Christie, K. Du, D. Banka, E. V. Schneider, A. Jestel, G. Zou, C. Si C. C. Ebmeier, R. T. Bronson, A. V. Krivtsov, A. G. Myers, N. E. Kohl, A. L. Kung, S. A. Armstrong, M. E. Lemieux, D. J. Taatjes, M. D. Shair
Mediator Kinase Inhibition Further Activates Super-Enhancer- Associated Genes In Aml
Nature V. 526 273 2015
PubMed-ID: 26416749  |  Reference-DOI: 10.1038/NATURE14904

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 8
    Chains: A
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN, RESIDUES 1-403
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 8, MEDIATOR COMPLEX SUBUNIT CDK8, MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT CDK8, PROTEIN KINASE K35, CDK8
 
Molecule 2 - CYCLIN-C
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SRB11 HOMOLOG, HSRB11, CYCLINC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1C1I1Ligand/IonCORTISTATIN A
2FMT5Ligand/IonFORMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , ALA A:50 , ILE A:79 , ASP A:98 , ALA A:100 , TRP A:105 , ALA A:155 , LEU A:158 , ARG A:356BINDING SITE FOR RESIDUE C1I A1360
2AC2SOFTWAREPRO A:124 , GLY A:126 , MET A:127 , HOH A:2070BINDING SITE FOR RESIDUE FMT A1361
3AC3SOFTWAREGLU A:101 , HIS A:102 , GLY A:161 , GLU A:162 , ILE A:351BINDING SITE FOR RESIDUE FMT A1362
4AC4SOFTWARELYS A:52 , GLU A:66 , PHE A:97 , ASP A:173BINDING SITE FOR RESIDUE FMT A1363
5AC5SOFTWAREALA B:74 , ARG B:75BINDING SITE FOR RESIDUE FMT B1265
6AC6SOFTWAREGLN B:49 , GLN B:59 , ALA B:63 , TYR B:156 , TYR B:184BINDING SITE FOR RESIDUE FMT B1266

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:176 -Ala A:177
2Asp A:338 -Pro A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CRL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhee....eeee...eeeeeeee........eeeeee.....hhhhhhhhhhhh.........eeeeeee....eeeeeee...eehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.........eee......hhhhh........hhhhhh.....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4crl A  -2 DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL 359
                                     7        17        27        37        47        57        67        77        87        97       107      |123       133       143       153       163       173       183||     203       213       223       233    || 250       260       270       280       290       300       310       320       330       340       350         
                                                                                                                                              114|                                                            184|                                        238|                                                                                                                 
                                                                                                                                               121                                                             195                                         246                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4crl B  -1 KAMAGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSVDMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPP 264
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
   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 4CRL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:338 - Pro A:339   [ RasMol ]  
    Phe A:176 - Ala A:177   [ RasMol ]  
 

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  CDK8_HUMAN | P49336
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CCNC_HUMAN | P24863: 3rgf 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp
        CDK8_HUMAN | P49336: 3rgf 4f6s 4f6u 4f6w 4f70 4f7j 4f7l 4f7n 4f7s 4g6l 5bnj 5cei 5fgk 5hbe 5hbh 5hbj 5hnb 5hvy 5i5z 5icp 5idn 5idp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CRL)