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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN LIVER X RECEPTOR BETA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC AGONIST
 
Authors :  S. Hoerer, A. Schmid, A. Heckel, R. M. Budzinski, H. Nar
Date :  13 Oct 03  (Deposition) - 20 Oct 04  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Receptor, Nuclear Hormone Receptor, Ligand Binding Domain, Liver X Receptor, Crystal Structure, Transcription Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hoerer, A. Schmid, A. Heckel, R. M. Budzinski, H. Nar
Crystal Structure Of The Human Liver X Receptor Beta Ligand-Binding Domain In Complex With A Synthetic Agonist
J. Mol. Biol. V. 334 853 2003
PubMed-ID: 14643652  |  Reference-DOI: 10.1016/J.JMB.2003.10.033

(-) Compounds

Molecule 1 - OXYSTEROLS RECEPTOR LXR-BETA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3
    Fragment: LIGAND BINDING DOMAIN, RESIDUES 209-461
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LIVER X RECEPTOR BETA, NUCLEAR ORPHAN, RECEPTOR LXR-BETA, UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR, NUCLEAR RECEPTOR NER

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
14441Ligand/IonN-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:268 , PHE A:271 , LEU A:274 , ALA A:275 , ILE A:309 , MET A:312 , LEU A:313 , THR A:316 , ILE A:327 , LEU A:345 , ILE A:353 , HIS A:435 , LEU A:442 , LEU A:449 , TRP A:457 , HOH A:2022 , HOH A:2031BINDING SITE FOR RESIDUE 444 A 462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UPV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UPV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UPV)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002537271aENSE00001386247chr19:50879685-50879833149NR1H2_HUMAN-00--
1.2ENST000002537272ENSE00001382965chr19:50879976-50880083108NR1H2_HUMAN-00--
1.3aENST000002537273aENSE00001124993chr19:50880844-5088090562NR1H2_HUMAN1-15150--
1.4ENST000002537274ENSE00000900338chr19:50880990-50881127138NR1H2_HUMAN15-61470--
1.5ENST000002537275ENSE00000900341chr19:50881406-50881696291NR1H2_HUMAN61-158980--
1.6ENST000002537276ENSE00000900344chr19:50881779-50882053275NR1H2_HUMAN158-249921A:219-250 (gaps)32
1.7ENST000002537277ENSE00000900347chr19:50882259-50882438180NR1H2_HUMAN250-309601A:251-31060
1.8ENST000002537278ENSE00000900350chr19:50883037-50883136100NR1H2_HUMAN310-343341A:311-34434
1.9bENST000002537279bENSE00000900352chr19:50885223-50885431209NR1H2_HUMAN343-412701A:344-41370
1.10cENST0000025372710cENSE00001124989chr19:50885713-50886266554NR1H2_HUMAN413-460481A:414-46148

(-) 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:232
 aligned with NR1H2_HUMAN | P55055 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:243
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457   
          NR1H2_HUMAN   218 QLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVHE 460
               SCOP domains d1upva_ A: Oxystero           ls receptor LXR-beta                                                                                                                                                                                                  SCOP domains
               CATH domains 1upvA00 A:219-461 R           etinoid X Receptor                                                                                                                                                                                                    CATH domains
               Pfam domains -----------------------------------Hormone_recep-1upvA01 A:254-449                                                                                                                                                                     ------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh-----------...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.....eehhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:219-250 (gaps) Exon 1.7  PDB: A:251-310 UniProt: 250-309                   Exon 1.8  PDB: A:311-344          ---------------------------------------------------------------------Exon 1.10c  PDB: A:414-461 UniProt: 413-460      Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:344-413 UniProt: 343-412                            ------------------------------------------------ Transcript 1 (2)
                 1upv A 219 QLTAAQELMIQQLVAAQLQ-----------VTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVHE 461
                                   228        |-         -|      258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458   
                                            237         249
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Hormone_recep] (290)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NR1H2_HUMAN | P55055)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0001133    RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.
    GO:0034191    apolipoprotein A-I receptor binding    Interacting selectively and non-covalently with an apolipoprotein A-I receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046965    retinoid X receptor binding    Interacting selectively and non-covalently with a retinoid X receptor.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    GO:0010887    negative regulation of cholesterol storage    Any process that decreases the rate or extent of cholesterol storage. Cholesterol storage is the accumulation and maintenance in cells or tissues of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0060336    negative regulation of interferon-gamma-mediated signaling pathway    Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
    GO:0032369    negative regulation of lipid transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010745    negative regulation of macrophage derived foam cell differentiation    Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:0048550    negative regulation of pinocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0032270    positive regulation of cellular protein metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
    GO:0010875    positive regulation of cholesterol efflux    Any process that increases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    GO:0032376    positive regulation of cholesterol transport    Any process that activates or increases the frequency, rate or extent of the directed movement of cholesterol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0045723    positive regulation of fatty acid biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0090108    positive regulation of high-density lipoprotein particle assembly    Any process that increases the frequency, rate, or extent of high-density lipoprotein particle assembly. High-density lipoprotein particle assembly is the aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle.
    GO:0010884    positive regulation of lipid storage    Any process that increases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0051006    positive regulation of lipoprotein lipase activity    Any process that activates or increases the activity of the enzyme lipoprotein lipase.
    GO:0090187    positive regulation of pancreatic juice secretion    Any process that increases the rate, frequency or extent of pancreatic juice secretion, the regulated release of pancreatic juice by the exocrine pancreas into the upper part of the intestine.
    GO:0090340    positive regulation of secretion of lysosomal enzymes    Any process that increases the rate, frequency or extent of secretion of lysosomal enzymes, the controlled release of lysosomal enzymes by a cell.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010867    positive regulation of triglyceride biosynthetic process    Any process that increases the rate, frequency, or extent of triglyceride biosynthesis. Triglyceride biosynthesis is the collection of chemical reactions and pathways resulting in the formation of triglyceride, any triester of glycerol.
    GO:2000188    regulation of cholesterol homeostasis    Any process that modulates the frequency, rate or extent of cholesterol homeostasis.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048384    retinoic acid receptor signaling pathway    The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NR1H2_HUMAN | P55055: 1p8d 1pq6 1pq9 1pqc 1upw 3kfc 3l0e 4dk7 4dk8 4nqa 4rak 5hjp 5i4v 5jy3 5kya 5kyj

(-) Related Entries Specified in the PDB File

1p8d X-RAY CRYSTAL STRUCTURE OF LXR LIGAND BINDING DOMAIN WITH24(S),25-EPOXYCHOLESTEROL
1pq6 HUMAN LXR BETA HORMONE RECEPTOR / GW3965 COMPLEX
1pq9 HUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317COMPLEX
1pqc HUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317
1upw CRYSTAL STRUCTURE OF THE HUMAN LIVER X RECEPTOR BETA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC AGONIST