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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SR12813-BOUND PXR/RXRALPHA LBD HETEROTETRAMER COMPLEX
 
Authors :  B. D. Wallace, L. Betts, M. R. Redinbo
Date :  10 Feb 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pregnane X Receptor, Retinoid X Receptor Alpha, Ligand Binding Domain, Nuclear Receptor, Sr12813, Alpha Helical Sandwich, Unique Intermolecular Beta-Sheet Dimerization, Xenobiotic Sensing, Upregulation Of Drug Metabolism Enzymes, Retinoic Acid-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Wallace, L. Betts, G. Talmage, R. M. Pollet, N. S. Holman, M. R. Redinbo
Structural And Functional Analysis Of The Human Nuclear Xenobiotic Receptor Pxr In Complex With Rxralpha.
J. Mol. Biol. V. 425 2561 2013
PubMed-ID: 23602807  |  Reference-DOI: 10.1016/J.JMB.2013.04.012

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA, NUCLEAR RECEPTOR COACTIVATOR 1
    Chains: D, C
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-AI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NR2B1, RXRA, BHLHE74, NCOA1, SRC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA, NCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID RECEPTOR COACTIVATOR 1, SRC-1
 
Molecule 2 - NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 2, NUCLEAR RECEPTOR COACTIVATOR 1
    Chains: A, B
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: BL21-AI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NR1I2, PXR, BHLHE74, NCOA1, SRC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ORPHAN NUCLEAR RECEPTOR PAR1, ORPHAN NUCLEAR RECEPTOR PXR, PREGNANE X RECEPTOR, STEROID AND XENOBIOTIC RECEPTOR, SXR, NCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID RECEPTOR COACTIVATOR 1, SRC-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SRL2Ligand/Ion[2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:206 , LEU A:209 , MET A:243 , MET A:246 , SER A:247 , GLN A:285 , PHE A:288 , TRP A:299 , TYR A:306 , MET A:323 , HIS A:407 , LEU A:411 , MET A:425BINDING SITE FOR RESIDUE SRL A 501
2AC2SOFTWARELEU B:209 , VAL B:211 , MET B:243 , SER B:247 , GLN B:285 , PHE B:288 , TRP B:299 , TYR B:306 , MET B:323 , HIS B:327 , HIS B:407 , MET B:425BINDING SITE FOR RESIDUE SRL B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5X)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5X)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh..ee..ee.....eeeee........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....ee.......ee........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5x A 141 QGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITSLTERHKILHRLLQE 458
                                   150       160       170      |194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       445       455   
                                                              177|                                                                                                                                                                                                                                             432|              
                                                               192                                                                                                                                                                                                                                              444              


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhh.....eeee.....eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee..eee..........hhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5x B 139 GVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGISSLTERHKILHRLLQEGS 460
                                   148       158       168       192       202       212       222       232       242       252       262       272       282       292       302       312|      326       336       346       356       366       376       386       396       406       416       426    || 447       457   
                                                                177|                                                                                                                     312|                                                                                                               431|                 
                                                                 192                                                                                                                      317                                                                                                                443                 


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains d4j5xc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh......ee.....ee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5x C 228 EDMPVERILEAELAVEPKTETYVEANMGLPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPRHKILHRLLQE 486
                                   237       247       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      |478        
                                                      256|                                                                                                                                                                                                  458|          
                                                       261                                                                                                                                                                                                   476          


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains d4j5xd_ D: automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.....ee....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5x D 228 EDMPVERILEAELAVEPKTETYVEANMGLNPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPRHKILHRLLQE 486
                                   237       247       257|      270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       477         
                                                       257|                                                                                                                                                                                                  458|          
                                                        261                                                                                                                                                                                                   476
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5X)

(-) Gene Ontology  (128, 165)

Asymmetric/Biological Unit(hide GO term definitions)

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  NR1I2_HUMAN | O75469
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  RXRA_HUMAN | P19793
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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA1_HUMAN | Q15788: 1fm6 1fm9 1k4w 1k74 1k7l 1kv6 1n4h 1nq7 1nrl 1p8d 1pzl 1rdt 1tfc 1u3r 1u3s 1x76 1x78 1x7b 1x7j 1xiu 1xv9 1xvp 1yy4 1yye 1zaf 2a3i 2c52 2fvj 2gtk 2hbh 2hc4 2hcd 2hfp 2npa 2nv7 2p54 2prg 3bej 3bqd 3ctb 3cwd 3dct 3dcu 3dr1 3et1 3et3 3fei 3fej 3fur 3fxv 3g8i 3g9e 3gyt 3gyu 3h0a 3hc5 3hc6 3hvl 3ipq 3ips 3ipu 3kmr 3lmp 3okh 3oki 3olf 3oll 3ols 3omk 3omm 3omo 3omp 3omq 3oof 3ook 3p88 3p89 3qt0 3rut 3ruu 3rvf 3s9s 3t03 3uu7 3uua 3uud 3v9y 3vn2 4dk7 4dk8 4dm6 4dm8 4dqm 4f9m 4fgy 4g1d 4g1y 4g1z 4g20 4g21 4g2h 4hee 4j5w 4jyg 4jyh 4jyi 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4ruj 4rup 4tuz 4tv1 4uda 4udb 4y29 5a86 5avi 5avl 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        NR1I2_HUMAN | O75469: 1ilg 1ilh 1m13 1nrl 1skx 2o9i 2qnv 3ctb 3hvl 3r8d 4j5w 4ny9 4s0s 4s0t 4x1f 4x1g 4xao 4xhd 5a86
        RXRA_HUMAN | P19793: 1by4 1dsz 1fby 1fm6 1fm9 1g1u 1g5y 1k74 1lbd 1mv9 1mvc 1mzn 1r0n 1rdt 1rxr 1xls 1xv9 1xvp 1ynw 2acl 2nll 2p1t 2p1u 2p1v 2zxz 2zy0 3dzu 3dzy 3e00 3e94 3fal 3fc6 3fug 3h0a 3kwy 3nsp 3nsq 3oap 3ozj 3pcu 3r29 3r2a 3r5m 3uvv 4cn2 4cn3 4cn5 4cn7 4j5w 4k4j 4k6i 4m8e 4m8h 4n5g 4n8r 4nqa 4oc7 4poh 4poj 4pp3 4pp5 4rfw 4rmc 4rmd 4rme 4zo1 4zsh 5ec9 5ji0 5lyq

(-) Related Entries Specified in the PDB File

4j5w