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 HUMAN NUCLEAR RECEPTOR SF-1 (NR5A1) BOUND TO ITS HORMONE PIP3 AT 2.4 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Stemcell)
Date :  04 Jun 14  (Deposition) - 30 Jul 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclear Hormone Receptor, Nr5A1, Sf-1 Ligand Bindingnuclear Domain, Regulatory Ligands, Transcription, Transcription Regulation, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Partnership For Stem Cell Biology, Pip3, Pip2, Nucleus, Nuclear Phosphatidylinositol Phosphates, Transcription Factor-Hormone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Blind, E. P. Sablin, K. M. Kuchenbecker, H. J. Chiu, A. M. Deacon, D. Das, R. J. Fletterick, H. A. Ingraham
The Signaling Phospholipid Pip3 Creates A New Interaction Surface On The Nuclear Receptor Sf-1.
Proc. Natl. Acad. Sci. Usa V. 111 15054 2014
PubMed-ID: 25288771  |  Reference-DOI: 10.1073/PNAS.1416740111

(-) Compounds

Molecule 1 - STEROIDOGENIC FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBH4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 218-461
    Gene: AD4BP, FTZF1, NR5A1, RC2003B, SF1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SF-1, STF-1, ADRENAL 4-BINDING PROTEIN, FUSHI TARAZU FACTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 1, STEROID HORMONE RECEPTOR AD4BP
 
Molecule 2 - PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA COACTIVATOR 1-ALPHA
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 139-152
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PGC-1ALPHA (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA CO-ACTIVATOR-1ALPHA) PEPTIDE CONTAINING RESIDUES 139- EEPSLLKKLLLAPA-152
    Synonym: PGC-1-ALPHA, PPAR-GAMMA COACTIVATOR 1-ALPHA, PPARGC-1-ALPHA, LIGAND EFFECT MODULATOR 6
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2PIZ1Ligand/Ion(2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIHEXADECANOATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:262 , LEU A:265 , LEU A:306 , VAL A:336 , GLN A:339 , ALA A:340 , GLY A:341 , LEU A:344 , ALA A:351 , TYR A:436 , LYS A:440 , HOH A:612 , HOH A:613 , HOH A:619 , HOH A:654 , HOH A:691 , HOH A:694 , HOH A:695 , HOH A:696BINDING SITE FOR RESIDUE PIZ A 501
2AC2SOFTWARETYR A:438 , LEU A:456 , GLN A:457 , HOH A:690 , HOH A:708BINDING SITE FOR RESIDUE ACT A 502
3AC3SOFTWARETHR A:272 , SER A:275 , ASP A:309 , HOH A:711BINDING SITE FOR RESIDUE ACT A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QJR)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qjr A 218 SGGPNVPELILQLLQLEPDEDQVRARILGSLQEPTKSRPDQPAAFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELTTVATQAGSLLHSLVLRAQELVLQLLALQLDRQEFVCLKFIILFSLDLKFLNNHILVKDAQEKANAALLDYTLCHYPHSGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAKQT 461
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457    


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4qjr B 141 PSLLKKLLLAPA 152
                                   150
   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 4QJR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (159, 171)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PIZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qjr)
 

(-) 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
  4qjr
    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
  PRGC1_HUMAN | Q9UBK2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  STF1_HUMAN | Q13285
    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
  PRGC1_HUMAN | Q9UBK2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  STF1_HUMAN | Q13285
    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
        PRGC1_HUMAN | Q9UBK2: 1xb7 3b1m 3cs8 3d24 3u9q 3v9t 3v9v 4qk4 5two
        STF1_HUMAN | Q13285: 1yow 1zdt 4qk4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QJR)