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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN BOUND TO THE HUMAN NR1D1 RESPONSE ELEMENT
 
Authors :  A. G. Mcewen, P. Poussin-Courmontagne, J. Osz, N. Rochel
Date :  21 Jan 14  (Deposition) - 18 Feb 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osz, A. G. Mcewen, P. Poussin-Courmontagne, E. Moutier, C. Birck, I. Davidson, D. Moras, N. Rochel
Structural Basis Of Natural Promoter Recognition By The Retinoid X Nuclear Receptor.
Sci. Rep. V. 5 8216 2015
PubMed-ID: 25645674  |  Reference-DOI: 10.1038/SREP08216

(-) Compounds

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHXGW
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: DNA-BINDING DOMAIN, RESIDUES 126-212
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA
 
Molecule 2 - 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3'
    Chains: C
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3'
    Chains: D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2K4Ligand/IonPOTASSIUM ION
3NO31Ligand/IonNITRATE ION
4ZN4Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:135 , CYS A:138 , CYS A:152 , CYS A:155BINDING SITE FOR RESIDUE ZN A1210
02AC2SOFTWARECYS A:171 , CYS A:177 , CYS A:187 , CYS A:190BINDING SITE FOR RESIDUE ZN A1211
03AC3SOFTWARECYS B:135 , CYS B:138 , CYS B:152 , CYS B:155BINDING SITE FOR RESIDUE ZN B1210
04AC4SOFTWARECYS B:171 , CYS B:177 , CYS B:187 , CYS B:190BINDING SITE FOR RESIDUE ZN B1211
05AC5SOFTWAREHOH B:2064 , HOH C:2027 , DT D:10 , DG D:11 , NO3 D:1019 , HOH D:2027BINDING SITE FOR RESIDUE K D1018
06AC6SOFTWAREDT C:13 , DC C:14 , HOH C:2046 , HOH C:2048BINDING SITE FOR RESIDUE K C1018
07AC7SOFTWAREDT C:6 , DC C:7 , HOH C:2016 , HOH C:2018 , HOH C:2064BINDING SITE FOR RESIDUE K C1019
08AC8SOFTWAREDA C:8 , DG C:9 , HOH C:2025 , HOH C:2033 , HOH C:2034BINDING SITE FOR RESIDUE K C1020
09AC9SOFTWAREHOH A:2083 , GLN B:206 , ARG B:209 , DG C:9 , DA C:10 , HOH C:2027 , DT D:10 , DG D:11 , K D:1018BINDING SITE FOR RESIDUE NO3 D1019
10BC1SOFTWARETYR A:169 , TYR A:189BINDING SITE FOR RESIDUE CL A1212
11BC2SOFTWARELYS A:181 , ARG A:182 , LEU A:196 , HOH A:2069 , HOH A:2103BINDING SITE FOR RESIDUE CL A1213
12BC3SOFTWAREGLN A:188 , HOH A:2046 , HOH A:2093 , DC D:9BINDING SITE FOR RESIDUE CL D1020
13BC4SOFTWARELYS B:160 , DT C:12 , DT C:13BINDING SITE FOR RESIDUE CL C1021
14BC5SOFTWAREARG A:172 , CYS A:187BINDING SITE FOR RESIDUE CL A1214

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CN5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CN5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CN5)

(-) Exons   (0, 0)

(no "Exon" information available for 4CN5)

(-) 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:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......ee.eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4cn5 A 129 MFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   138       148       158       168       178       188       198       208 


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4cn5 B 132 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   141       151       161       171|      184       194       204     
                                                                 171|                                  
                                                                  175                                  


Chain C from PDB  Type:DNA  Length:17
                                                 
                 4cn5 C   1 TGGGGTCAGAGTTCAAT  17
                                    10       


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4cn5 D   1 ATTGAACTCTGACCCCA  17
                                    10
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  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 4CN5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CN5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CN5)

(-) Gene Ontology  (78, 78)

Asymmetric/Biological Unit(hide GO term definitions)

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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
        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 4cn7 4j5w 4j5x 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

4cn2 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN RAMP2 RESPONSE ELEMENT
4cn3 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN GDE1SPA RESPONSE ELEMENT
4cn7 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO AN IDEALIZED DR1 RESPONSE ELEMENT