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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN CHROMOBOX HOMOLOG 3 (CBX3)
 
Authors :  M. F. Amaya, M. Ravichandran, P. Loppnau, I. Kozieradzki, A. M. Edwards C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Bochkarev, J. Min, H. Ouya Structural Genomics Consortium (Sgc)
Date :  27 Sep 11  (Deposition) - 07 Mar 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,T
Keywords :  Structural Genomics Consortium, Sgc, Chromatin Regulator, Nucleus, Phosphoprotein, Repressor, Transcription Regulation, Transcription- Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ruan, H. Ouyang, M. F. Amaya, M. Ravichandran, P. Loppnau, J. Min, J. Zang
Structural Basis Of The Chromodomain Of Cbx3 Bound To Methylated Peptides From Histone H1 And G9A.
Plos One V. 7 35376 2012
PubMed-ID: 22514736  |  Reference-DOI: 10.1371/JOURNAL.PONE.0035376

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 3
    Chains: A
    Engineered: YES
    Fragment: UNP RESIDUES 29-81
    Gene: CBX3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HECH, HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA, HP1 GAMMA, MODIFIER 2 PROTEIN
 
Molecule 2 - HISTONE H1.4
    Chains: T
    Engineered: YES
    Fragment: UNP RESIDUES 19-36
    Gene: HIST1H1E, H1F4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H1B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 3TZD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TZD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CBX3_HUMAN30-88
121-179		  1A:30-81
-
2CHROMO_1PS00598 Chromo domain signature.CBX3_HUMAN47-67  1A:47-67

(-) Exons   (0, 0)

(no "Exon" information available for 3TZD)

(-) 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:58
 aligned with CBX3_HUMAN | Q13185 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:74
                                    17        27        37        47        57        67        77    
            CBX3_HUMAN    8 LQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK 81
               SCOP domains d3tzd                a_ A: automated matches                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....----------------eeeeeeeeeeeee..eeeeeeee...hhhhheeee...eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CHROMO_2  PDB: A:30-81 UniProt: 30-88                PROSITE (1)
                PROSITE (2) ---------------------------------------CHROMO_1  PDB: A:47-6-------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------- Transcript
                  3tzd A 24 LYFQG----------------EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK 81
                                |    -         - |      37        47        57        67        77    
                               28               29                                                    


Chain T from PDB  Type:PROTEIN  Length:12
 aligned with H14_HUMAN | P10412 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:12
                                    27  
             H14_HUMAN   18 TPVKKKARKSAG 29
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .....eee.... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                  3tzd T 18 YPVKKKARkSAG 29
                                    27  
                                   26-MLY
   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 beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TZD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain T   (H14_HUMAN | P10412)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    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).
biological process
    GO:0098532    histone H3-K27 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 27 of the histone.
    GO:0080182    histone H3-K4 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
    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:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0016584    nucleosome positioning    Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another.
    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.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX3_HUMAN | Q13185: 2l11 3dm1 3kup 5t1i
        H14_HUMAN | P10412: 5jjz

(-) Related Entries Specified in the PDB File

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