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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT HUMAN ROR GAMMA LIGAND BINDING DOMAIN WITH ROCKOGENIN.
 
Authors :  M. Noguchi, A. Nomura, K. Murase, S. Doi, K. Yamaguchi, T. Adachi
Date :  03 Mar 17  (Deposition) - 07 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Inhibitor, Ternary Complex, Nuclear Receptor, Transferase-Ihibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Noguchi, A. Nomura, K. Murase, S. Doi, K. Yamaguchi, K. Hirata, M. Shiozaki, S. Hirashima, M. Kotoku, T. Yamaguchi, Y. Katsuda, R. Steensma, X. Li, H. Tao, B. Tse, M. Fenn, R. Babine, E. Bradley, P. Crowe, S. Thacher, T. Adachi, M. Kamada
Ternary Complex Of Human Ror Gamma Ligand-Binding Domain, Inverse Agonist And Smrt Peptide Shows A Unique Mechanism O Corepressor Recruitment
Genes Cells V. 22 535 2017
PubMed-ID: 28493531  |  Reference-DOI: 10.1111/GTC.12494

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR ROR-GAMMA
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 261-518
    Gene: RORC, NR1F3, RORG, RZRG
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR RZR-GAMMA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP F MEMBER 3,RAR-RELATED ORPHAN RECEPTOR C,RETINOID-RELATED ORPHAN RECEPTOR-GAMMA
 
Molecule 2 - NUCLEAR RECEPTOR COREPRESSOR 2
    Chains: B, D, F, H
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Fragment: UNP RESIDUES 2346-2367
    Gene: NCOR2, CTG26
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: N-COR2,CTG REPEAT PROTEIN 26,SMAP270,SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR,SMRT,T3 RECEPTOR- ASSOCIATING FACTOR,TRAC,THYROID-,RETINOIC-ACID-RECEPTOR-ASSOCIATED COREPRESSOR

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
182R4Ligand/Ion(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-TETRAMETHYLSPIRO[5-OXAPENTACYCLO[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]ICOSANE-6,2'-OXANE]-10,16-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
182R1Ligand/Ion(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-TETRAMETHYLSPIRO[5-OXAPENTACYCLO[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]ICOSANE-6,2'-OXANE]-10,16-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
182R1Ligand/Ion(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-TETRAMETHYLSPIRO[5-OXAPENTACYCLO[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]ICOSANE-6,2'-OXANE]-10,16-DIOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
182R1Ligand/Ion(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-TETRAMETHYLSPIRO[5-OXAPENTACYCLO[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]ICOSANE-6,2'-OXANE]-10,16-DIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
182R1Ligand/Ion(1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-TETRAMETHYLSPIRO[5-OXAPENTACYCLO[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]ICOSANE-6,2'-OXANE]-10,16-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:285 , GLN A:286 , CYS A:320 , VAL A:361 , ARG A:364 , PHE A:377 , PHE A:378 , PHE A:388binding site for residue 82R A 9000
2AC2SOFTWARECYS C:285 , GLN C:286 , HIS C:323 , ALA C:327 , ARG C:364 , ARG C:367 , PHE C:377 , PHE C:378 , PHE C:388 , ILE C:397binding site for residue 82R C 9000
3AC3SOFTWARECYS E:285 , GLN E:286 , HIS E:323 , LEU E:324 , ALA E:327 , ARG E:364 , PHE E:377 , PHE E:378 , PHE E:388binding site for residue 82R E 9000
4AC4SOFTWARECYS G:285 , GLN G:286 , CYS G:320 , LEU G:324 , VAL G:361 , ARG G:364 , ARG G:367 , PHE G:377 , PHE G:388 , ILE G:397 , ILE G:400binding site for residue 82R G 9000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X8Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X8Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X8Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X8Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5X8Q)

(-) 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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8q A  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain B from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                5x8q B 2345 TNMGLEAIIRKALMG 2359
                                  2354     


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8q C  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain D from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5x8q D 2346 NMGLEAIIRKALMG 2359
                                  2355    


Chain E from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8q E  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain F from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5x8q F 2346 NMGLEAIIRKALMG 2359
                                  2355    


Chain G from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8q G  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain H from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                5x8q H 2345 TNMGLEAIIRKALMG 2359
                                  2354
   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 5X8Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X8Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X8Q)

(-) Gene Ontology  (53, 59)

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  5x8q
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  RORG_HUMAN | P51449
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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOR2_HUMAN | Q9Y618: 1kkq 1r2b 1xc5 2gpv 2l5g 2ltp 2odd 2rt5 3r29 3r2a 4a69 4oar 5x8x
        RORG_HUMAN | P51449: 3b0w 3kyt 3l0j 3l0l 4nb6 4nie 4qm0 4s14 4wlb 4wpf 4wqp 4xt9 4ymq 4ypq 4zjr 4zjw 4zom 5aph 5apj 5apk 5ayg 5c4o 5c4s 5c4t 5c4u 5ejv 5eth 5g42 5g43 5g44 5g45 5g46 5ixk 5iz0 5k38 5k3l 5k3m 5k3n 5k6e 5k74 5lwp 5m96 5nti 5ntk 5ntn 5ntp 5ntq 5ntw 5nu1 5ufo 5ufr 5uhi 5vb3 5vb5 5vb6 5vb7

(-) Related Entries Specified in the PDB File

5x8s 5x8u 5x8w 5x8x