Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 ID2 HLH HOMODIMER AT 2.1A RESOLUTION
 
Authors :  M. V. Wong, S. Jiang, P. Palasingam, P. R. Kolatkar
Date :  19 Jun 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. V. Wong, S. Jiang, P. Palasingam, P. R. Kolatkar
A Divalent Ion Is Crucial In The Structure And Dominant- Negative Function Of Id Proteins, A Class Of Helix-Loop- Helix Transcription Regulators.
Plos One V. 7 48591 2012
PubMed-ID: 23119064  |  Reference-DOI: 10.1371/JOURNAL.PONE.0048591

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN INHIBITOR ID-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST-565
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentHELIX-LOOP-HELIX DOMAIN, RESIDUES 1-82
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCLASS D BASIC HELIX-LOOP-HELIX PROTEIN 26, CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 26, BHLHB26, INHIBITOR OF DNA BINDING 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2K2Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:47 , VAL A:50 , PRO A:51 , ILE A:53 , GLN A:55 , HOH A:2001BINDING SITE FOR RESIDUE K A1089
2AC2SOFTWAREMET A:39 , LYS A:61 , TYR B:43 , LYS B:61BINDING SITE FOR RESIDUE ACT A1090
3AC3SOFTWARELYS B:47 , VAL B:50 , PRO B:51 , ILE B:53 , GLN B:55 , HOH B:2007BINDING SITE FOR RESIDUE K B1083

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AYA)

(-) Exons   (0, 0)

(no "Exon" information available for 4AYA)

(-) 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:59
 aligned with ID2_HUMAN | Q02363 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:84
                                    39        49        59        69        79        89        99       109    
            ID2_HUMAN    30 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHPTIVSLHHQRPGQNQASRTPLTTLNTDISIL 113
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.--------...-----------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4aya A  30 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH--------LKP-----------------SFL  88
                                    39        49        59        69        79  |      - | |     -         - |  
                                                                               82       83 |                86  
                                                                                          85                    

Chain B from PDB  Type:PROTEIN  Length:48
 aligned with ID2_HUMAN | Q02363 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:48
                                    44        54        64        74        
            ID2_HUMAN    35 LLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH  82
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 4aya B  35 LLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSH  82
                                    44        54        64        74        

   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 4AYA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ID2_HUMAN | Q02363)
molecular function
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0048541    Peyer's patch development    The process whose specific outcome is the progression of Peyer's patches over time, from their formation to the mature structure. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes.
    GO:0060612    adipose tissue development    The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat.
    GO:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0003166    bundle of His development    The process whose specific outcome is the progression of the bundle of His over time, from its formation to the mature structure. The bundle of His is part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    GO:0048667    cell morphogenesis involved in neuron differentiation    The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron.
    GO:0071285    cellular response to lithium ion    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 lithium (Li+) ion stimulus.
    GO:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    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:0048557    embryonic digestive tract morphogenesis    The process in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0061031    endodermal digestive tract morphogenesis    The process in which the anatomical structures of the endodermal digestive tract are generated and organized. The endodermal digestive tract includes those portions of the digestive tract that are derived from endoderm.
    GO:0009649    entrainment of circadian clock    The synchronization of a circadian rhythm to environmental time cues such as light.
    GO:0043153    entrainment of circadian clock by photoperiod    The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
    GO:0043353    enucleate erythrocyte differentiation    The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
    GO:0061030    epithelial cell differentiation involved in mammary gland alveolus development    The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland alveolus.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0002521    leukocyte differentiation    The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
    GO:0045475    locomotor rhythm    The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
    GO:0060749    mammary gland alveolus development    The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
    GO:0033598    mammary gland epithelial cell proliferation    The multiplication or reproduction of mammary gland epithelial cells, resulting in the expansion of a cell population. Mammary gland epithelial cells make up the covering of surfaces of the mammary gland. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
    GO:0003149    membranous septum morphogenesis    The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    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:0001779    natural killer cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
    GO:0045578    negative regulation of B cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0010629    negative regulation of gene expression    Any process that decreases 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:2000178    negative regulation of neural precursor cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0048715    negative regulation of oligodendrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of oligodendrocyte differentiation.
    GO:0045668    negative regulation of osteoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0048663    neuron fate commitment    The process in which the developmental fate of a cell becomes restricted such that it will develop into a neuron.
    GO:0021772    olfactory bulb development    The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex.
    GO:0014003    oligodendrocyte development    The process aimed at the progression of an oligodendrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An oligodendrocyte is a type of glial cell involved in myelinating the axons in the central nervous system.
    GO:0048711    positive regulation of astrocyte differentiation    Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
    GO:0045777    positive regulation of blood pressure    Any process in which the force of blood traveling through the circulatory system is increased.
    GO:0071158    positive regulation of cell cycle arrest    Any process that increases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0045600    positive regulation of fat cell differentiation    Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
    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:0045651    positive regulation of macrophage differentiation    Any process that activates or increases the frequency, rate or extent of macrophage differentiation.
    GO:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    GO:0071931    positive regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that activates or increases transcription as part of the G1/S transition of the mitotic cell cycle.
    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:2000045    regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    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:0019216    regulation of lipid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    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:0001966    thigmotaxis    The directed movement of a motile cell or organism in response to touch.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4aya)
 

(-) 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
  4aya
    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
  ID2_HUMAN | Q02363
    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)
  (no 'MIM ID' available)
    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
  ID2_HUMAN | Q02363
    Protein Disorder PredictionDisEMBL | 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 4AYA)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4AYA)