Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 VDR LBD IN COMPLEX WITH 2ALPHA-METHYL CALCITRIOL
 
Authors :  S. Hourai, N. Rochel, D. Moras
Date :  14 Jun 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Helical Sandwich, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Hourai, T. Fujishima, A. Kittaka, Y. Suhara, H. Takayama, N. Rochel, D. Moras
Probing A Water Channel Near The A-Ring Of Receptor-Bound 1Alpha, 25-Dihydroxyvitamin D3 With Selected 2Alpha-Substituted Analogues
J. Med. Chem. V. 49 5199 2006
PubMed-ID: 16913708  |  Reference-DOI: 10.1021/JM0604070
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVITAMIN D NUCLEAR RECEPTOR, VDR, 1,25- DIHYDROXYVITAMIN D3 RECEPTOR

 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
1MVD1Ligand/Ion2ALPHA-METHYL-1ALPHA,25-DIHYDROXY-VITAMIN D3

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , LEU A:227 , VAL A:234 , SER A:237 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , CYS A:288 , HIS A:305 , LEU A:309 , HIS A:397BINDING SITE FOR RESIDUE MVD A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HB8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:373 -Pro A:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029309L230VVDR_HUMANPolymorphism11574090AL230V
2UniProtVAR_004664R274LVDR_HUMANDisease (VDDR2A)121909796AR274L
3UniProtVAR_004665H305QVDR_HUMANDisease (VDDR2A)121909798AH305Q
4UniProtVAR_004666I314SVDR_HUMANDisease (VDDR2A)121909799AI314S
5UniProtVAR_029310T362IVDR_HUMANPolymorphism11574115AT362I
6UniProtVAR_004667R391CVDR_HUMANDisease (VDDR2A)121909800AR391C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HB8)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003953241ENSE00001485612chr12:48298814-4829873877VDR_HUMAN-00--
1.3ENST000003953243ENSE00001354497chr12:48276557-4827647781VDR_HUMAN-00--
1.4ENST000003953244ENSE00000888048chr12:48272898-48272751148VDR_HUMAN1-49490--
1.5ENST000003953245ENSE00000738168chr12:48258960-48258830131VDR_HUMAN49-93450--
1.6ENST000003953246ENSE00000738167chr12:48251471-48251287185VDR_HUMAN93-154621A:119-15436
1.7ENST000003953247ENSE00000738166chr12:48251032-48250912121VDR_HUMAN155-195411A:155-16410
1.8ENST000003953248ENSE00000738165chr12:48249584-48249413172VDR_HUMAN195-252581A:216-25237
1.9ENST000003953249ENSE00000738164chr12:48240591-48240440152VDR_HUMAN252-303521A:252-30352
1.10ENST0000039532410ENSE00000738163chr12:48240234-48240118117VDR_HUMAN303-342401A:303-34240
1.11ENST0000039532411ENSE00001419012chr12:48238788-482353223467VDR_HUMAN342-427861A:342-42382

(-) 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:254
 aligned with VDR_HUMAN | P11473 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:305
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     
            VDR_HUMAN   119 SLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHCITSSDMMDSSSFSNLDLSEEDSDDPSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
               SCOP domains d2hb8a_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2hb8A00 A:119-423 Retinoid X Receptor                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh.....hhhhh...........---------------------------------------------------hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------V-------------------------------------------L------------------------------Q--------S-----------------------------------------------I----------------------------C-------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:119-154            Exon 1.7  PDB: A:155-164 UniProt: 155-195-----------------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:303-342               --------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.8  PDB: A:216-252 UniProt: 195-252 [INCOMPLETE]    -----------------------------------------------------------------------------------------Exon 1.11  PDB: A:342-423 UniProt: 342-427 [INCOMPLETE]                            Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:252-303 UniProt: 252-303           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (3)
                 2hb8 A 119 SLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGG---------------------------------------------------SVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
                                   128       138       148       158     |   -         -         -         -         -       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     
                                                                       164                                                 216                                                                                                                                                                                                               

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HB8)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VDR_HUMAN | P11473)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:1902098    calcitriol binding    Interacting selectively and non-covalently with calcitriol. Calcitriol (1,25-dihydroxycholecalciferol) is the hormonally active form of vitamin D3.
    GO:0008434    calcitriol receptor activity    Combining with calcitriol, the hormonally active form of vitamin D3, 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:1902121    lithocholic acid binding    Interacting selectively and non-covalently with lithocholic acid.
    GO:0038186    lithocholic acid receptor activity    Combining with lithocholic acid and transmitting the signal to initiate a change in cell activity.
    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:0070644    vitamin D response element binding    Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0038183    bile acid signaling pathway    A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000902    cell morphogenesis    The developmental process in which the size or shape of a cell is generated and organized.
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0046697    decidualization    The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta.
    GO:0050892    intestinal absorption    Any process in which nutrients are taken up from the contents of the intestine.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0060745    mammary gland branching involved in pregnancy    The process in which the branching structure of the mammary gland duct is generated and organized as a part of pregnancy.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010839    negative regulation of keratinocyte proliferation    Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
    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:0060058    positive regulation of apoptotic process involved in mammary gland involution    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process of mammary epithelial cells during mammary gland involution.
    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:0045618    positive regulation of keratinocyte differentiation    Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation.
    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:0010980    positive regulation of vitamin D 24-hydroxylase activity    Any process that increases the rate, frequency or extent of vitamin D 24-hydroxylase activity. Vitamin D 24-hydroxylase activity catalyzes the hydroxylation of C-24 of any form of vitamin D.
    GO:0060558    regulation of calcidiol 1-monooxygenase activity    Any process that modulates the rate, frequency or extent of calcidiol 1-monooxygenase activity. Calcidiol 1-monooxygenase activity is catalysis of the reaction: calcidiol + NADPH + H+ + O2 = calcitriol + NADP+ + H2O.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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.
    GO:0070561    vitamin D receptor signaling pathway    The series of molecular signals generated as a consequence of a vitamin D receptor binding to one of its physiological ligands.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    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.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

 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
    MVD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:373 - Pro A:374   [ RasMol ]  
 

(-) 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
  2hb8
    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
  VDR_HUMAN | P11473
    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)
  277440
    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
  VDR_HUMAN | P11473
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VDR_HUMAN | P114731db1 1ie8 1ie9 1kb2 1kb4 1kb6 1s0z 1s19 1txi 1ynw 2ham 2har 2has 2hb7 3a2i 3a2j 3a3z 3a40 3a78 3auq 3aur 3ax8 3az1 3az2 3az3 3b0t 3cs4 3cs6 3kpz 3m7r 3ogt 3p8x 3tkc 3vhw 3w0a 3w0c 3w0y 3wgp 3wwr 3x31 3x36 4g2i 4ite 4itf 5gt4

(-) Related Entries Specified in the PDB File

1db1 1ie8 1ie9 1s0z 1s19 2ham 2har 2has 2hb7