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(-) Description

Title :  COMPLEX STRUCTURES OF CBP BROMODOMAIN WITH H4 ACK20 PEPTIDE
 
Authors :  L. Zeng, Q. Zhang, G. Gerona-Navarro, M. M. Zhou
Date :  03 Feb 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Bromodomain, Histone, Creb, Cbp, P53, Acetylation, Activator, Chromosomal Rearrangement, Disease Mutation, Host-Virus Interaction, Metal-Binding, Methylation, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Transferase, Zinc, Zinc-Finger, Chromosomal Protein, Dna- Binding, Nucleosome Core, Transferase/Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zeng, Q. Zhang, G. Gerona-Navarro, N. Moshkina, M. M. Zhou
Structural Basis Of Site-Specific Histone Recognition By The Bromodomains Of Human Coactivators Pcaf And Cbp/P300
Structure V. 16 643 2008
PubMed-ID: 18400184  |  Reference-DOI: 10.1016/J.STR.2008.01.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CREB-BINDING PROTEIN
    ChainsA
    EC Number2.3.1.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantBL21
    Expression System VectorPET15B
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 1081-1197
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - HISTONE H4
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantBL21
    Expression System VectorPET15B
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 14-28
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE

(-) Sites  (0, 0)

(no "Site" information available for 2RNY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037305Y1175CCBP_HUMANDisease (RSTS1)28937315AY1175C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H4PS00047 Histone H4 signature.H4_HUMAN15-19  1B:14-18
2BROMODOMAIN_2PS50014 Bromodomain profile.CBP_HUMAN1103-1175  1A:1103-1175
3BROMODOMAIN_1PS00633 Bromodomain signature.CBP_HUMAN1108-1167  1A:1108-1167

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002623671aENSE00001871332chr16:3930722-3929833890CBP_HUMAN1-29290--
1.2ENST000002623672ENSE00001789080chr16:3901010-3900298713CBP_HUMAN29-2662380--
1.3ENST000002623673ENSE00001788865chr16:3860780-3860604177CBP_HUMAN267-325590--
1.4ENST000002623674ENSE00001744566chr16:3843627-3843387241CBP_HUMAN326-406810--
1.5ENST000002623675ENSE00001693899chr16:3842095-3841982114CBP_HUMAN406-444390--
1.6ENST000002623676ENSE00001692816chr16:3832927-3832685243CBP_HUMAN444-525820--
1.7ENST000002623677ENSE00001608958chr16:3831307-3831205103CBP_HUMAN525-559350--
1.8ENST000002623678ENSE00001732416chr16:3830879-3830733147CBP_HUMAN559-608500--
1.9ENST000002623679ENSE00001656158chr16:3828818-3828701118CBP_HUMAN608-647400--
1.10ENST0000026236710ENSE00001678454chr16:3828183-3828012172CBP_HUMAN648-705580--
1.11ENST0000026236711ENSE00001615007chr16:3827658-382761445CBP_HUMAN705-720160--
1.12ENST0000026236712ENSE00001733259chr16:3824694-3824570125CBP_HUMAN720-761420--
1.13ENST0000026236713ENSE00001638447chr16:3823931-3823752180CBP_HUMAN762-821600--
1.14ENST0000026236714ENSE00001594624chr16:3820987-3820571417CBP_HUMAN822-9601390--
1.15ENST0000026236715ENSE00001625302chr16:3819354-3819175180CBP_HUMAN961-1020600--
1.16ENST0000026236716ENSE00001784635chr16:3817910-3817721190CBP_HUMAN1021-1084641A:1077-1084 (gaps)16
1.17ENST0000026236717ENSE00001709420chr16:3808973-3808855119CBP_HUMAN1084-1123401A:1084-112340
1.18ENST0000026236718ENSE00001644140chr16:3808049-3807810240CBP_HUMAN1124-1203801A:1124-119774
1.19ENST0000026236719ENSE00001699420chr16:3807377-380728989CBP_HUMAN1204-1233300--
1.20ENST0000026236720ENSE00001592013chr16:3801807-380172781CBP_HUMAN1233-1260280--
1.21ENST0000026236721ENSE00001789918chr16:3799684-379962857CBP_HUMAN1260-1279200--
1.22ENST0000026236722ENSE00001670717chr16:3795355-379527878CBP_HUMAN1279-1305270--
1.23ENST0000026236723ENSE00001684253chr16:3794962-379489568CBP_HUMAN1305-1328240--
1.24ENST0000026236724ENSE00001804031chr16:3790550-3790400151CBP_HUMAN1328-1378510--
1.25ENST0000026236725ENSE00001623920chr16:3789725-3789579147CBP_HUMAN1378-1427500--
1.26ENST0000026236726ENSE00001698951chr16:3788673-3788560114CBP_HUMAN1427-1465390--
1.27ENST0000026236727ENSE00000894975chr16:3786816-3786651166CBP_HUMAN1465-1520560--
1.28ENST0000026236728ENSE00000894970chr16:3786204-3786037168CBP_HUMAN1521-1576560--
1.29ENST0000026236729ENSE00001062588chr16:3781938-3781777162CBP_HUMAN1577-1630540--
1.30ENST0000026236730ENSE00000865712chr16:3781474-3781193282CBP_HUMAN1631-1724940--
1.31ENST0000026236731ENSE00001292463chr16:3779875-37750554821CBP_HUMAN1725-24427180--

2.1ENST000003778031ENSE00001475159chr6:26104104-26104518415H4_HUMAN1-1271271B:13-2715

(-) Sequences/Alignments

NMR Structure
   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:121
 aligned with CBP_HUMAN | Q92793 from UniProtKB/Swiss-Prot  Length:2442

    Alignment length:129
                                  1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188         
           CBP_HUMAN   1069 GTASQSTSPSQPRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG 1197
               SCOP domains d        2rnya_ A: CREB-binding protein, CBP                                                                                      SCOP domains
               CATH domains 2        rnyA00 A:1077-1197 Histone Acetyltransferase; Chain A                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh............hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------C---------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------BROMODOMAIN_2  PDB: A:1103-1175 UniProt: 1103-1175                       ---------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------BROMODOMAIN_1  PDB: A:1108-1167 UniProt: 1108-1167          ------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.16       ---------------------------------------Exon 1.18  PDB: A:1124-1197 UniProt: 1124-1203 [INCOMPLETE]                Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.17  PDB: A:1084-1123             -------------------------------------------------------------------------- Transcript 1 (2)
                2rny A 1077 G--------SHMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG 1197
                            |     1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188         
                            |     1078                                                                                                                       
                         1077                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:15
                                    23     
            H4_HUMAN     14 GGAKRHRKVLRDNIQ   28
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE -HISTO--------- PROSITE
               Transcript 2 Exon 2.1        Transcript 2
                2rny B   13 GGAKRHRkVLRDNIQ   27
                                   |22     
                                  20-ALY   

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RNY)

(-) Gene Ontology  (92, 97)

NMR Structure(hide GO term definitions)
Chain A   (CBP_HUMAN | Q92793)
molecular function
    GO:0043426    MRF binding    Interacting selectively and non-covalently with Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors.
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0016407    acetyltransferase activity    Catalysis of the transfer of an acetyl group to an acceptor molecule.
    GO:0033613    activating transcription factor binding    Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0034212    peptide N-acetyltransferase activity    Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide.
    GO:0042975    peroxisome proliferator activated receptor binding    Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma.
    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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0018076    N-terminal peptidyl-lysine acetylation    The acetylation of the N-terminal lysine of proteins.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0098609    cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules.
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0034644    cellular response to UV    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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0042592    homeostatic process    Any biological process involved in the maintenance of an internal steady state.
    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:1900087    positive regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:1901224    positive regulation of NIK/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of NIK/NF-kappaB signaling.
    GO:0060355    positive regulation of cell adhesion molecule production    Any process that increases the rate, frequency or extent of cell adhesion molecule production. Cell adhesion molecule production is the appearance of a cell adhesion molecule as a result of its biosynthesis or a decrease in its catabolism.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0032481    positive regulation of type I interferon production    Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0008589    regulation of smoothened signaling pathway    Any process that modulates the frequency, rate or extent of smoothened signaling.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain B   (H4_HUMAN | P62805)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0034080    CENP-A containing nucleosome assembly    The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core 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. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    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:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBP_HUMAN | Q927931jsp 1liq 1rdt 1wo3 1wo4 1wo5 1wo6 1wo7 1zoq 2d82 2kje 2kwf 2l84 2l85 2lxs 2lxt 2n1a 3dwy 3p1c 3p1d 3p1e 3p1f 3svh 4a9k 4n3w 4n4f 4nr4 4nr5 4nr6 4nr7 4nyv 4nyw 4nyx 4ouf 4tqn 4ts8 4whu 4yk0 5cgp 5dbm 5eic 5eng 5ep7 5gh9 5h85 5i83 5i86 5i89 5i8b 5i8g 5j0d 5jem 5ktu 5ktw 5ktx 5mpz 5mqe 5mqg 5mqk 5tb6
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RNY)