Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN BOUND TO THE HUMAN GDE1SPA 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 :  2.35
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  B,C,G,H  (1x)
Biol. Unit 2:  A,D,E,F  (1x)
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
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHXGW
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN, RESIDUES 130-212
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA
 
Molecule 2 - RETINOIC ACID RECEPTOR RXR-ALPHA
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHXGW
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN, RESIDUES 130-212
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA
 
Molecule 3 - 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
    ChainsE, G
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 4 - 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
    ChainsF, H
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x) BC   GH
Biological Unit 2 (1x)A  DEF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:135 , CYS A:138 , CYS A:152 , CYS A:155BINDING SITE FOR RESIDUE ZN A1209
2AC2SOFTWARECYS A:171 , CYS A:177 , CYS A:187 , CYS A:190BINDING SITE FOR RESIDUE ZN A1210
3AC3SOFTWARECYS B:135 , CYS B:138 , CYS B:152 , CYS B:155BINDING SITE FOR RESIDUE ZN B1209
4AC4SOFTWARECYS B:171 , CYS B:177 , CYS B:187 , CYS B:190BINDING SITE FOR RESIDUE ZN B1210
5AC5SOFTWARECYS C:135 , CYS C:138 , CYS C:152 , CYS C:155BINDING SITE FOR RESIDUE ZN C1210
6AC6SOFTWARECYS C:171 , CYS C:177 , CYS C:187 , CYS C:190BINDING SITE FOR RESIDUE ZN C1211
7AC7SOFTWARECYS D:135 , CYS D:138 , CYS D:152 , CYS D:155BINDING SITE FOR RESIDUE ZN D1210
8AC8SOFTWARECYS D:171 , CYS D:177 , CYS D:187 , CYS D:190BINDING SITE FOR RESIDUE ZN D1211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CN3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CN3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CN3)

(-) Exons   (0, 0)

(no "Exon" information available for 4CN3)

(-) 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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4cn3 A 131 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 208
                                   140       150       160       170       180       190       200        

Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4cn3 B 133 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 208
                                   142       152       162       172       182       192       202      

Chain C from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eee..eeehhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4cn3 C 126 GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   135       145       155       165       175       185       195       205    

Chain D from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4cn3 D 132 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDDKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   141       151       161       171       181       191       201        

Chain E from PDB  Type:DNA  Length:17
                                                 
                 4cn3 E   1 CTAGTTCAAAGTTCACA  17
                                    10       

Chain F from PDB  Type:DNA  Length:17
                                                 
                 4cn3 F   1 TGTGAACTTTGAACTAG  17
                                    10       

Chain G from PDB  Type:DNA  Length:17
                                                 
                 4cn3 G   1 CTAGTTCAAAGTTCACA  17
                                    10       

Chain H from PDB  Type:DNA  Length:17
                                                 
                 4cn3 H   1 TGTGAACTTTGAACTAG  17
                                    10       

   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 4CN3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CN3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CN3)

(-) Gene Ontology  (78, 78)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cn3)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4cn3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RXRA_HUMAN | P19793
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RXRA_HUMAN | P19793
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RXRA_HUMAN | P197931by4 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 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

4cn2 CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN RAMP2 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