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(-) Description

Title :  CRYSTAL STRUCTURE OF REV-ERB BETA
 
Authors :  E. -J. Woo, D. G. Jeong, M. -Y. Lim, S. Jun Kim, S. Eon Ryu
Date :  19 May 07  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Zinc, Receptor, Repressor, Zinc-Finger, Dna-Binding, Constitutive Repression, Transcription Regulation, Orphan Receptor, A-Helical Sandwich, Transcription, Metal-Binding, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. -J. Woo, D. G. Jeong, M. -Y. Lim, S. Jun Kim, K. -J. Kim, S. -M. Yoon, B. -C. Park, S. Eon Ryu
Structural Insight Into The Constitutive Repression Function Of The Nuclear Receptor Rev-Erbbeta
J. Mol. Biol. V. 373 735 2007
PubMed-ID: 17870090  |  Reference-DOI: 10.1016/J.JMB.2007.08.037

(-) Compounds

Molecule 1 - ORPHAN NUCLEAR RECEPTOR NR1D2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid511693
    FragmentLIGAND-BINDING DOMAIN, RESIDUES 386-579
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEAR-1R, ORPHAN NUCLEAR HORMONE RECEPTOR BD73, REV-ERB BETA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2V0V)

(-) Sites  (0, 0)

(no "Site" information available for 2V0V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V0V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V0V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V0V)

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003125211aENSE00001730590chr3:23986751-23987085335NR1D2_HUMAN1-660--
1.3aENST000003125213aENSE00001261140chr3:23996028-23996294267NR1D2_HUMAN6-95900--
1.4ENST000003125214ENSE00001203459chr3:23997528-2399761689NR1D2_HUMAN95-124300--
1.5aENST000003125215aENSE00001699264chr3:24001162-24001306145NR1D2_HUMAN125-173490--
1.6bENST000003125216bENSE00001203450chr3:24003468-24004096629NR1D2_HUMAN173-3822100--
1.8bENST000003125218bENSE00001670863chr3:24006468-24006653186NR1D2_HUMAN383-444624A:396-444
B:396-444
C:398-444
D:398-444
49
49
47
47
1.9bENST000003125219bENSE00001701951chr3:24009304-24009514211NR1D2_HUMAN445-515714A:445-515
B:445-515
C:445-515
D:445-515
71
71
71
71
1.10cENST0000031252110cENSE00001293494chr3:24018714-240212372524NR1D2_HUMAN515-579654A:515-576
B:515-576
C:515-576
D:515-576
62
62
62
62

(-) 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:181
 aligned with NR1D2_HUMAN | Q14995 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:181
                                   405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575 
          NR1D2_HUMAN   396 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....ee...................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8b  PDB: A:396-444 UniProt: 383-444       ----------------------------------------------------------------------Exon 1.10c  PDB: A:515-576 UniProt: 515-579 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.9b  PDB: A:445-515 UniProt: 445-515                             ------------------------------------------------------------- Transcript 1 (2)
                 2v0v A 396 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLGSKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
                                   405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575 

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with NR1D2_HUMAN | Q14995 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:181
                                   405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575 
          NR1D2_HUMAN   396 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....ee...........hhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8b  PDB: B:396-444 UniProt: 383-444       ----------------------------------------------------------------------Exon 1.10c  PDB: B:515-576 UniProt: 515-579 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.9b  PDB: B:445-515 UniProt: 445-515                             ------------------------------------------------------------- Transcript 1 (2)
                 2v0v B 396 KSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLGSKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
                                   405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575 

Chain C from PDB  Type:PROTEIN  Length:179
 aligned with NR1D2_HUMAN | Q14995 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:179
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567         
          NR1D2_HUMAN   398 GHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee...ee............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8b  PDB: C:398-444 UniProt: 383-444     ----------------------------------------------------------------------Exon 1.10c  PDB: C:515-576 UniProt: 515-579 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.9b  PDB: C:445-515 UniProt: 445-515                             ------------------------------------------------------------- Transcript 1 (2)
                 2v0v C 398 GHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLGSKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567         

Chain D from PDB  Type:PROTEIN  Length:179
 aligned with NR1D2_HUMAN | Q14995 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:179
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567         
          NR1D2_HUMAN   398 GHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Hormone_recep-2v0vD01 D:398-576                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) Hormone_recep-2v0vD02 D:398-576                                                                                                                                                     Pfam domains (2)
           Pfam domains (3) Hormone_recep-2v0vD03 D:398-576                                                                                                                                                     Pfam domains (3)
           Pfam domains (4) Hormone_recep-2v0vD04 D:398-576                                                                                                                                                     Pfam domains (4)
         Sec.struct. author ....hhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh........ee...ee....hhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8b  PDB: D:398-444 UniProt: 383-444     ----------------------------------------------------------------------Exon 1.10c  PDB: D:515-576 UniProt: 515-579 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.9b  PDB: D:445-515 UniProt: 445-515                             ------------------------------------------------------------- Transcript 1 (2)
                 2v0v D 398 GHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLGSKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
                                   407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567         

   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 2V0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V0V)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NR1D2_HUMAN | Q14995)
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:0001046    core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:2000505    regulation of energy homeostasis    Any process that modulates the frequency, rate or extent of energy homeostasis.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0019216    regulation of lipid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    GO:2001014    regulation of skeletal muscle cell differentiation    Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    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.
cellular component
    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
        NR1D2_HUMAN | Q149952v7c 3cqv 4n73

(-) Related Entries Specified in the PDB File

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