Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN BOUND TO THE HUMAN RAMP2 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 :  2.07
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription-Dna Complex, Nuclear Receptor (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: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHXGW
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN, RESIDUES 130-212
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA, RETINOID X RECEPTOR
 
Molecule 2 - 5'-D(*TP*GP*AP*GP*TP*TP*CP*AP*AP*GP*GP*GP*TP*DC *AP*AP*TP)-3'
    Chains: A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*TP*TP*GP*AP*CP*CP*CP*TP*TP*GP*AP*AP*DC *TP*CP*AP)-3'
    Chains: B
    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, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG7Ligand/IonMAGNESIUM ION
4ZN4Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS C:135 , CYS C:138 , CYS C:152 , CYS C:155BINDING SITE FOR RESIDUE ZN C1211
02AC2SOFTWARECYS C:171 , CYS C:177 , CYS C:187 , CYS C:190BINDING SITE FOR RESIDUE ZN C1212
03AC3SOFTWARETHR C:162 , ASP C:166 , LEU C:167 , THR C:168 , TYR C:169 , TYR C:189 , TYR C:192 , GLN C:193 , ARG C:202BINDING SITE FOR RESIDUE MES C1213
04AC4SOFTWARECYS D:135 , CYS D:138 , CYS D:152 , CYS D:155BINDING SITE FOR RESIDUE ZN D1213
05AC5SOFTWARECYS D:171 , CYS D:177 , CYS D:187 , CYS D:190BINDING SITE FOR RESIDUE ZN D1214
06AC6SOFTWAREARG D:172 , CYS D:187 , GLN D:188BINDING SITE FOR RESIDUE CL D1215
07AC7SOFTWAREVAL C:149 , TYR C:150 , HOH D:2025BINDING SITE FOR RESIDUE CL C1214
08AC8SOFTWAREHOH B:2019 , HOH B:2020 , GLN D:206 , ARG D:209BINDING SITE FOR RESIDUE CL D1216
09AC9SOFTWARETYR D:169 , THR D:170 , ARG D:186BINDING SITE FOR RESIDUE CL D1217
10BC1SOFTWAREDG B:11 , DA B:12 , ASP C:140 , CYS C:152 , GLU C:153 , GLY C:154 , ARG C:184 , MG C:1217BINDING SITE FOR RESIDUE MG C1215
11BC2SOFTWARELEU C:196 , GLY C:199 , MET C:200 , LYS C:201BINDING SITE FOR RESIDUE MG C1216
12BC3SOFTWAREDT A:1 , DG A:2 , HOH A:2039 , GLY C:144 , LYS C:145BINDING SITE FOR RESIDUE MG A1035
13BC4SOFTWAREDT B:3 , DG B:4 , GLY D:154 , PHE D:158 , ARG D:161BINDING SITE FOR RESIDUE MG D1218
14BC5SOFTWAREDA B:12 , ASP C:140 , LYS C:181 , ARG C:184 , MG C:1215 , HOH C:2037BINDING SITE FOR RESIDUE MG C1217
15BC6SOFTWAREDG A:10 , HOH A:2029 , HIS D:146BINDING SITE FOR RESIDUE MG A1036
16BC7SOFTWAREDT B:9 , HOH B:2031 , HOH B:2032 , LYS C:165BINDING SITE FOR RESIDUE MG B1035

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CN2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CN2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CN2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CN2)

(-) Exons   (0, 0)

(no "Exon" information available for 4CN2)

(-) 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:DNA  Length:17
                                                 
                 4cn2 A   1 TGAGTTCAAGGGTCAAT  17
                                    10       


Chain B from PDB  Type:DNA  Length:17
                                                 
                 4cn2 B   1 ATTGACCCTTGAACTCA  17
                                    10       


Chain C from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......ee.eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4cn2 C 129 MFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ 210
                                   138       148       158       168       178       188       198       208  


Chain D from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4cn2 D 132 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG 212
                                   141       151       161       171       181       191       201       211
   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 4CN2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CN2)

(-) Gene Ontology  (78, 78)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cn2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4cn2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RXRA_HUMAN | P19793
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RXRA_HUMAN | P19793
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4cn3 4cn5 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

4cn3 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN GDE1SPA RESPONSE ELEMENT
4cn5 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN NR1D1 RESPONSE ELEMENT
4cn7 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO AN IDEALIZED DR1 RESPONSE ELEMENT