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(-) Description

Title :  STRUCTURAL BASIS FOR THE HIERARCHICAL ASSEMBLY OF THE CORE OF PRC1.1
 
Authors :  S. J. Wong, A. B. Taylor, P. J. Hart, C. A. Kim
Date :  20 Apr 16  (Deposition) - 14 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gene Repression, Complex, Transcription Regulation, Transcription Repressor, Metal Binding Protein-Transcription Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Wong, M. D. Gearhart, A. B. Taylor, D. R. Nanyes, D. J. Ha, A. K. Robinson, J. A. Artigas, O. J. Lee, B. Demeler, P. J. Hart, V. J. Bardwell, C. A. Kim
Kdm2B Recruitment Of The Polycomb Group Complex, Prc1. 1, Requires Cooperation Between Pcgf1 And Bcorl1.
Structure V. 24 1795 2016
PubMed-ID: 27568929  |  Reference-DOI: 10.1016/J.STR.2016.07.011

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 2B
    Chains: A
    EC Number: 1.14.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1059-1336
    Gene: KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CXXC-TYPE ZINC FINGER PROTEIN 2,F-BOX AND LEUCINE-RICH REPEAT PROTEIN 10,F-BOX PROTEIN FBL10,F-BOX/LRR-REPEAT PROTEIN 10, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1B,JUMONJI DOMAIN-CONTAINING EMSY-INTERACTOR METHYLTRANSFERASE MOTIF PROTEIN, PROTEIN JEMMA,PROTEIN-CONTAINING CXXC DOMAIN 2,[HISTONE-H3]-LYSINE-36 DEMETHYLASE 1B
 
Molecule 2 - S-PHASE KINASE-ASSOCIATED PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 2-163
    Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYCLIN-A/CDK2-ASSOCIATED PROTEIN P19,P19A,ORGAN OF CORTI PROTEIN 2,OCP-2,ORGAN OF CORTI PROTEIN II,OCP-II,RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN,SIII,TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1-LIKE,P19SKP1
 
Molecule 3 - POLYCOMB GROUP RING FINGER PROTEIN 1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 150-255
    Gene: PCGF1, NSPC1, RNF68
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NERVOUS SYSTEM POLYCOMB-1,NSPC1,RING FINGER PROTEIN 68
 
Molecule 4 - BCL-6 COREPRESSOR-LIKE PROTEIN 1
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1594-1711
    Gene: BCORL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCOR-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric/Biological Unit (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5JH5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JH5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser C:246 -Pro C:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JH5)

(-) Exons   (0, 0)

(no "Exon" information available for 5JH5)

(-) 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:267
                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhh...hhhhhh.hhhhh.eee.......hhhhhhhhhhhh..eee......hhhhhhhhhhhh....eee....hhhhhhhhhh.......eee.......hhhhhhhhhh................eee......hhhhhhhhhhhh....eee.......hhhhhhhhh...hhhhhhh.eee........hhhhhhhh......eee.......hhhhhhhhhhhhh....ee.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jh5 A 1065 mHREVWmAVFSYLSHQDLCVCmRVCRTWNRWCCDKRLWTRIDLNHCKSITPLmLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQmRDLLSPPTDNRPNRSKLRNIVELRLAGLDITDASLRLIIRHmPLLSKLHLSYCNHVTDQSINLLTAVGTTTRDSLTEINLSDCNKVTDQCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEmSVSVQFGQVEEKLLQKL 1335
                            |     1074      1084 |    1094      1104      1114  |   1124      1134      1144      1154      1164      1174      1184      1194      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328       
                            |     |           1086-MSE                       1117-MSE                                                                  1191-MSE    1203|                         1237-MSE                                                                         1318-MSE             
                         1065-MSE |                                                                                                                                 1208                                                                                                                               
                               1071-MSE                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeehhhhh.hhhhhhhhhhh...ee....hhhhhhhhhhhhhhh..................hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jh5 B    2 PSIKLQSSDGEIFEVDVEIAKQSVTIKTmLEDLGmPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDNKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANmIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQW  159
                                    11        21        31    ||  48        58        68     || 80        90       100       110       120     | 130       140       150         
                                                       30-MSE ||                            74|                                              126-MSE                             
                                                             36-MSE                          77                                                                                  
                                                              44                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:88
                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeeeeee...eeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                5jh5 C  157 HSKAHYYRYDEQLNLCLERLSNKYVRCSVRAEVRHLRRVLCHRLmLNPQHVQLLFDNEVLPDHmTmKQIWLSRWFGKPSPLLLQYSVK  255
                                   166       176||     197       207    |  217       227   | | 237       247        
                                              177|                    212-MSE            231-MSE                    
                                               189                                         233-MSE                  


Chain D from PDB  Type:PROTEIN  Length:105
                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeee........eeeeehhhhhhhhh.hhhhhhhhh....eeeeehhhhhhhhhh............eeeeee.hhhhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                5jh5 D 1594 DDFmFELSDKPLLPCYNLQVSVSRGPCNWFLFSDVLKRLKLSSRIFQARFPHFEITTmPKAEFYRQVASSQLLTPAERPGETVELVRYEPDLLRLLGSEVEFQSC 1709
                               |  1603      1613      1623      1633      1643      1653      1663      1673|     1694      1704     
                            1597-MSE                                              1651-MSE              1673|                        
                                                                                                         1685
   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 5JH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JH5)

(-) Gene Ontology  (59, 77)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ser C:246 - Pro C:247   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        BCORL_HUMAN | Q5H9F3: 4hpm
        KDM2B_HUMAN | Q8NHM5: 4o64
        PCGF1_HUMAN | Q9BSM1: 4hpl 4hpm
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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JH5)