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(-) Description

Title :  STRUCTURE OF THE AML1-ETO NERVY DOMAIN - PKA(RIIA) COMPLEX AND ITS CONTRIBUTION TO AML1-ETO ACTIVITY
 
Authors :  T. A. Corpora, T. Cierpecki, J. Bushweller
Date :  25 May 10  (Deposition) - 20 Oct 10  (Release) - 20 Oct 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (15x)
NMR Structure *:  A,B,C  (1x)
Keywords :  Protein/Protein, Homodimer Bound To Monomer, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Corpora, L. Roudaia, Z. M. Oo, W. Chen, E. Manuylova, X. Cai, M. J. Chen, T. Cierpicki, N. A. Speck, J. H. Bushweller
Structure Of The Aml1-Eto Nhr3-Pka(Riialpha) Complex And It Contribution To Aml1-Eto Activity.
J. Mol. Biol. V. 402 560 2010
PubMed-ID: 20708017  |  Reference-DOI: 10.1016/J.JMB.2010.08.007

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS PARALLEL 2
    Expression System Taxid562
    Expression System VectorPLASMID
    GenePRKAR2A, PKR2, PRKAR2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - PROTEIN CBFA2T1
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-32A
    Expression System Taxid562
    Expression System VectorPLASMID
    GeneRUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN MTG8, PROTEIN ETO, EIGHT TWENTY ONE PROTEIN, CYCLIN- D-RELATED PROTEIN, ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  123
NMR Structure (15x)ABC
NMR Structure * (1x)ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KYG)

(-) Sites  (0, 0)

(no "Site" information available for 2KYG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KYG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KYG)

(-) Exons   (4, 5)

NMR Structure (4, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002655631aENSE00001926435chr3:48885279-48884768512KAP2_HUMAN1-88882A:-2-44
B:-2-44
45
45
1.2ENST000002655632ENSE00001335223chr3:48845117-4884508236KAP2_HUMAN88-100130--
1.3aENST000002655633aENSE00001321402chr3:48831482-4883143053KAP2_HUMAN100-117180--
1.4bENST000002655634bENSE00001318834chr3:48828060-4882797784KAP2_HUMAN118-145280--
1.5ENST000002655635ENSE00001296318chr3:48820525-48820419107KAP2_HUMAN146-181360--
1.6ENST000002655636ENSE00001315035chr3:48810541-48810388154KAP2_HUMAN181-232520--
1.7bENST000002655637bENSE00001169115chr3:48802782-48802681102KAP2_HUMAN233-266340--
1.8ENST000002655638ENSE00000768107chr3:48802511-4880243775KAP2_HUMAN267-291250--
1.9ENST000002655639ENSE00000768105chr3:48793877-4879381266KAP2_HUMAN292-313220--
1.10bENST0000026556310bENSE00000768103chr3:48789750-48789609142KAP2_HUMAN314-361480--
1.11dENST0000026556311dENSE00001841831chr3:48789151-487840125140KAP2_HUMAN361-404440--

2.6bENST000002658146bENSE00001297181chr8:93088364-93088193172MTG8_HUMAN1-30300--
2.11lENST0000026581411lENSE00001782570chr8:93029591-93029454138MTG8_HUMAN30-76470--
2.12nENST0000026581412nENSE00002197259chr8:93027048-93026807242MTG8_HUMAN76-156810--
2.13cENST0000026581413cENSE00001682869chr8:93023319-9302323090MTG8_HUMAN157-186300--
2.14eENST0000026581414eENSE00001706185chr8:93017525-93017344182MTG8_HUMAN187-247610--
2.17bENST0000026581417bENSE00001739575chr8:93004117-93003867251MTG8_HUMAN247-331850--
2.18bENST0000026581418bENSE00001770404chr8:92999200-9299911586MTG8_HUMAN331-359290--
2.19ENST0000026581419ENSE00001764658chr8:92998553-92998352202MTG8_HUMAN360-427681C:578-584 (gaps)11
2.21ENST0000026581421ENSE00001658814chr8:92988201-9298813369MTG8_HUMAN427-450241C:585-59814
2.22cENST0000026581422cENSE00001768415chr8:92983076-92982886191MTG8_HUMAN450-513641C:598-61518
2.23hENST0000026581423hENSE00001226380chr8:92972745-929711521594MTG8_HUMAN514-604910--

(-) 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:50
 aligned with KAP2_HUMAN | P13861 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:50
                                 1                                            
                                 |   5        15        25        35        45
           KAP2_HUMAN     - -----MSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA  45
               SCOP domains d2kyga_ A: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
               Transcript 1 -----Exon 1.1a  PDB: A:-2-44 UniProt: 1-88         Transcript 1
                 2kyg A  -7 GAMGSMSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA  44
                                  || 4        14        24        34        44
                                 -1|                                          
                                   2                                          

Chain B from PDB  Type:PROTEIN  Length:50
 aligned with KAP2_HUMAN | P13861 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:50
                                 1                                            
                                 |   5        15        25        35        45
           KAP2_HUMAN     - -----MSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA  45
               SCOP domains d2kygb_ B: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
           Pfam domains (1) ------------RIIa-2kygB01 B:7-44                    Pfam domains (1)
           Pfam domains (2) ------------RIIa-2kygB02 B:7-44                    Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
               Transcript 1 -----Exon 1.1a  PDB: B:-2-44 UniProt: 1-88         Transcript 1
                 2kyg B  -7 GAMGSMSHIQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREARA  44
                                  || 4        14        24        34        44
                                 -1|                                          
                                   2                                          

Chain C from PDB  Type:PROTEIN  Length:38
 aligned with MTG8_HUMAN | Q06455 from UniProtKB/Swiss-Prot  Length:604

    Alignment length:70
                                   407       417       427       437       447       457       467
           MTG8_HUMAN   398 DAEDLKKGGGSSSSHSRQQSPVNPDPVALDAHREFLHRPASGYVPEEIWKKAEEAVNEVKRQAMTELQKA 467
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....----..----------------------------......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.19 UniProt: 360-427    ----------------------Exon 2.22c         Transcript 2 (1)
           Transcript 2 (2) -----------------------------Exon 2.21  PDB: C:585-59----------------- Transcript 2 (2)
                 2kyg C 578 AMADI----GS----------------------------ASGYVPEEIWKKAEEAVNEVKRQAMTELQKA 615
                                |  583|        -         -       585       595       605       615
                              582  583|                          585                              
                                    584                                                           

   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, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KYG)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: RIIa (3)

(-) Gene Ontology  (38, 40)

NMR Structure(hide GO term definitions)
Chain A,B   (KAP2_HUMAN | P13861)
molecular function
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0004862    cAMP-dependent protein kinase inhibitor activity    Stops, prevents or reduces the activity of a cAMP-dependent protein kinase.
    GO:0008603    cAMP-dependent protein kinase regulator activity    Modulation of the activity of the enzyme cAMP-dependent protein kinase.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
    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:0034199    activation of protein kinase A activity    Any process that initiates the activity of the inactive enzyme protein kinase A.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0071377    cellular response to glucagon 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 glucagon stimulus.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:2000480    negative regulation of cAMP-dependent protein kinase activity    Any process that stops, prevents or reduces the frequency, rate or extent of cAMP-dependent protein kinase activity.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0003091    renal water homeostasis    Renal process involved in the maintenance of an internal steady state of water in the body.
cellular component
    GO:0005952    cAMP-dependent protein kinase complex    An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.
    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:0097546    ciliary base    Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031588    nucleotide-activated protein kinase complex    A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0044853    plasma membrane raft    A membrane raft that is part of the plasma membrane.

Chain C   (MTG8_HUMAN | Q06455)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive 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.
biological process
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAP2_HUMAN | P138612izx 4zp3 5h77 5h78 5xby
        MTG8_HUMAN | Q064551wq6 2dj8 2h7b 2knh 2od1 2odd 2pp4 4jol

(-) Related Entries Specified in the PDB File

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