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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CBX3 CHROMO SHADOW DOMAIN
 
Authors :  W. Tempel, Z. Li, Y. Li, I. Kozieradzki, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, H. Ouyang, Structural Genomics Consortium (Sgc)
Date :  27 Nov 09  (Deposition) - 08 Dec 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Chromo Shadow Domain, Structural Genomics Consortium, Sgc, Acetylation, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Tempel, Z. Li, Y. Li, I. Kozieradzki, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, H. Ouyang
Crystal Structure Of The Cbx3 Chromo Shadow Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 3
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-MHL
    Expression System Strain: BL21 (DE3)_V2R
    Expression System Taxid: 469008
    Fragment: CHROMO SHADOW DOMAIN (UNP RESIDUES 110-173)
    Gene: CBX3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA, HP1 GAMMA, MODIFIER 2 PROTEIN, HECH

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1UNX6Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1UNX2Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1UNX4Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3KUP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KUP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys B:113 -Pro B:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KUP)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
121-179
 
 
 		  4-
A:121-172
B:121-173
C:121-172
D:121-173
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
121-179
 
 
 		  2-
A:121-172
B:121-173
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
121-179
 
 
 		  2-
-
-
C:121-172
D:121-173

(-) Exons   (0, 0)

(no "Exon" information available for 3KUP)

(-) 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:59
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:59
                                   123       133       143       153       163         
           CBX3_HUMAN   114 PRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
               SCOP domains d3kupa_ A: automated matches                                SCOP domains
               CATH domains 3kupA00 A:114-172  [code=2.40.50.40, no name defined]       CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CHROMO_2  PDB: A:121-172 UniProt: 121-179            PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 3kup A 114 PRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
                                   123       133       143       153       163         


Chain B from PDB  Type:PROTEIN  Length:62
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:62
                                   121       131       141       151       161       171  
           CBX3_HUMAN   112 DKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
               SCOP domains d3kupb_ B: automated matches                                   SCOP domains
               CATH domains 3kupB00 B:112-173  [code=2.40.50.40, no name defined]          CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeee..........eeeeee.....eeeeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CHROMO_2  PDB: B:121-173 UniProt: 121-179             PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 3kup B 112 DKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
                                   121       131       141       151       161       171  


Chain C from PDB  Type:PROTEIN  Length:59
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:61
                                   121       131       141       151       161       171 
           CBX3_HUMAN   112 DKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
               SCOP domains d3kupc_ C: automated   matches                                SCOP domains
               CATH domains 3kupC00 C:112-172  [  code=2.40.50.40, no name defined]       CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeeeee.--...eeeeee.....eeeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CHROMO_2  PDB: C:121-172 UniProt: 121-179            PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 3kup C 112 DKPRGFARGLDPERIIGATD--GELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
                                   121       131  |    141       151       161       171 
                                             131  |                                      
                                                134                                      


Chain D from PDB  Type:PROTEIN  Length:60
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:60
                                   123       133       143       153       163       173
           CBX3_HUMAN   114 PRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
               SCOP domains d3kupd_ D: automated matches                                 SCOP domains
               CATH domains 3kupD00 D:114-173  [code=2.40.50.40, no name defined]        CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------CHROMO_2  PDB: D:121-173 UniProt: 121-179             PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 3kup D 114 PRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
                                   123       133       143       153       163       173
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KUP)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CBX3_HUMAN | Q13185)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:1990226    histone methyltransferase binding    Interacting selectively and non-covalently with a histone methyltransferase enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0071549    cellular response to dexamethasone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dexamethasone stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    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: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:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000779    condensed chromosome, centromeric region    The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005719    nuclear euchromatin    The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    GO:0005637    nuclear inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
    GO:0031618    nuclear pericentric heterochromatin    Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    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:0035985    senescence-associated heterochromatin focus    A transcriptionally-silent heterochromatin structure present in senescent cells. Contains the condensed chromatin of one chromosome and is enriched for histone modifications. Thought to repress expression of proliferation-promoting genes.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX3_HUMAN | Q13185: 2l11 3dm1 3tzd 5t1i

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