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

(-) Description

Title :  UNWINDING THE DIFFERENCES OF THE MAMMALIAN PERIOD CLOCK PROTEINS FROM CRYSTAL STRUCTURE TO CELLULAR FUNCTION
 
Authors :  E. Wolf, N. Kucera, S. Hennig
Date :  01 Feb 12  (Deposition) - 29 Feb 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pas Domain, Circadian Rhythm, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kucera, I. Schmalen, S. Hennig, R. Ollinger, H. M. Strauss, A. Grudziecki, C. Wieczorek, A. Kramer, E. Wolf
Unwinding The Differences Of The Mammalian Period Clock Proteins From Crystal Structure To Cellular Function.
Proc. Natl. Acad. Sci. Usa V. 109 3311 2012
PubMed-ID: 22331899  |  Reference-DOI: 10.1073/PNAS.1113280109

(-) Compounds

Molecule 1 - PERIOD CIRCADIAN PROTEIN HOMOLOG 3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PER3
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MPER3, CIRCADIAN CLOCK PROTEIN PERIOD 3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DJ3)

(-) Sites  (0, 0)

(no "Site" information available for 4DJ3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DJ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DJ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DJ3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.PER3_MOUSE280-326
 		  2A:280-326
B:280-326

(-) Exons   (0, 0)

(no "Exon" information available for 4DJ3)

(-) 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:298
 aligned with PER3_MOUSE | O70361 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:308
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403        
           PER3_MOUSE   104 AHQADVTVYSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRGFLKSVHFVDLLAPQDVRAFYAHTAPTQLPFWNNWTQRASQYECAPAKPFFCRICGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCLTLVEKIHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLNEDVFATRIKKAASNDKDIAELQEQIHKLLLQPV 411
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhh....eeeeeee.....eeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.........----------......eeeee...........eeeeeeeeeee..........eeeeeeeee..........hhhh.eeeeee.....eeee..hhhhhhh.hhhhhh..hhhhhh.....hhhhhhhhhhhhh.....ee...eeee.....eeeeeeeeeeee......eeeeeeeeee....................hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAS  PDB: A:280-326 UniProt: 280-326           ------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dj3 A 104 GRLEDVTVYSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRGFLKSVHFVDLLAPQDVRAFYAHTAPTQLPFWN----------CAPAKPFFCRICGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCLTLVEKIHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLNEDVFATRIKKAASNDKDIAELQEQIHKLLLQPV 411
                                   113       123       133       143       153       163       173       183       | -       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403        
                                                                                                                 191        202                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with PER3_MOUSE | O70361 from UniProtKB/Swiss-Prot  Length:1113

    Alignment length:293
                                   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   
           PER3_MOUSE   119 ALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRGFLKSVHFVDLLAPQDVRAFYAHTAPTQLPFWNNWTQRASQYECAPAKPFFCRICGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCLTLVEKIHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLNEDVFATRIKKAASNDKDIAELQEQIHKLLLQPV 411
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee......eeee..........--------.hhhhhhhhhhhhhhhhh...........----------....eeee..-----......eeeeeeee........--....eeeeeee..........hhhh.eeeeee.....eeee...hhhhhh.hhhhhh..hhhhhh.....hhhhhhhhhhhhh..........eeee.....eeeeeeeeeeee......eeeeeeeeee................---....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------PAS  PDB: B:280-326 UniProt: 280-326           ------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dj3 B 119 ALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNS--------HFVDLLAPQDVRAFYAHTAPTQLPFWNNW----------PAKPFFCRIC-----EKRHYSPFRILPYLVHVHSSAQ--PEPCCLTLVEKIHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLNEDVFATRIKK---NDKDIAELQEQIHKLLLQPV 411
                                   128       138       148       | -      |168       178       188    |    -     | 208    |    -|      228       238 |  |  248       258       268       278       288       298       308       318       328       338       348       358       368       378       388   |   398       408   
                                                               156      165                         193        204      213   219                  240  |                                                                                                                                              388 392                   
                                                                                                                                                      243
   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 4DJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DJ3)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PER3_MOUSE | O70361)
molecular function
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    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:0045187    regulation of circadian sleep/wake cycle, sleep    Any process that modulates the frequency, rate or extent of sleep; a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
    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: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: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.

 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
(no "Ligands, Modified Residues, Ions" information available for 4dj3)
 
  Sites
(no "Sites" information available for 4dj3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dj3)
 

(-) 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 ](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
  4dj3
    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
  PER3_MOUSE | O70361
    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
  PER3_MOUSE | O70361
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4DJ3)

(-) Related Entries Specified in the PDB File

1wa9 DROSOPHILA PERIOD
3gdi MOUSE PERIOD 2
4dj2 MOUSE PERIOD 1