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(-) Description

Title :  EPHA2 DIMERIC STRUCTURE IN THE LIPIDIC BICELLE AT PH 5.0
 
Authors :  M. L. Mayzel, E. V. Bocharov, P. E. Volynsky, A. S. Arseniev
Date :  27 Oct 08  (Deposition) - 11 Aug 09  (Release) - 16 Mar 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (17x)
Keywords :  Receptor Tyrosine Kinase, Membrane Protein, Dimeric Transmembrane Domain, Ephrin Receptor, Atp-Binding, Glycoprotein, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Polymorphism, Receptor, Transferase, Transmembrane, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. V. Bocharov, M. L. Mayzel, P. E. Volynsky, K. S. Mineev, E. N. Tkach, Y. S. Ermolyuk, A. A. Schulga, R. G. Efremov, A. S. Arseniev
Left-Handed Dimer Of Epha2 Transmembrane Domain: Helix Packing Diversity Among Receptor Tyrosine Kinases
Biophys. J. V. 98 881 2010
PubMed-ID: 20197042  |  Reference-DOI: 10.1016/J.BPJ.2009.11.008

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 2
    ChainsA, B
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEMEX1
    Expression System Vector TypeVECTOR
    FragmentEPHA2_TM, RESIDUES 523-563
    GeneEPHA2, ECK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTYROSINE-PROTEIN KINASE RECEPTOR ECK, EPITHELIAL CELL KINASE

 Structural Features

(-) Chains, Units

  
NMR Structure (17x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K9Y)

(-) Sites  (0, 0)

(no "Site" information available for 2K9Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K9Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K9Y)

(-) Exons   (3, 6)

NMR Structure (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003584321aENSE00001954971chr1:16482582-16482343240EPHA2_HUMAN1-29290--
1.2ENST000003584322ENSE00000827996chr1:16477458-1647739168EPHA2_HUMAN29-51230--
1.3ENST000003584323ENSE00001031821chr1:16475542-16474873670EPHA2_HUMAN52-2752240--
1.5ENST000003584325ENSE00000827994chr1:16464925-16464770156EPHA2_HUMAN275-327530--
1.6ENST000003584326ENSE00000955420chr1:16464680-16464348333EPHA2_HUMAN327-4381120--
1.7ENST000003584327ENSE00000955397chr1:16462265-16462150116EPHA2_HUMAN438-476390--
1.8ENST000003584328ENSE00001031787chr1:16461684-16461531154EPHA2_HUMAN477-528522A:523-528
B:523-528
6
6
1.9bENST000003584329bENSE00001031795chr1:16461062-16460963100EPHA2_HUMAN528-561342A:528-561
B:528-561
34
34
1.10ENST0000035843210ENSE00000955400chr1:16460410-1646035556EPHA2_HUMAN561-580202A:561-563
B:561-563
3
3
1.11aENST0000035843211aENSE00001031771chr1:16460101-16459976126EPHA2_HUMAN580-622430--
1.12aENST0000035843212aENSE00000955402chr1:16459863-16459675189EPHA2_HUMAN622-685640--
1.13ENST0000035843213ENSE00000955403chr1:16458934-1645887362EPHA2_HUMAN685-705210--
1.14ENST0000035843214ENSE00000955404chr1:16458768-16458559210EPHA2_HUMAN706-775700--
1.15ENST0000035843215ENSE00000955405chr1:16458365-16458216150EPHA2_HUMAN776-825500--
1.16ENST0000035843216ENSE00000955406chr1:16456914-16456721194EPHA2_HUMAN826-890650--
1.17ENST0000035843217ENSE00001031824chr1:16456084-16455929156EPHA2_HUMAN890-942530--
1.18bENST0000035843218bENSE00001840165chr1:16451815-16450832984EPHA2_HUMAN942-976350--

(-) 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:41
 aligned with EPHA2_HUMAN | P29317 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:41
                                   532       542       552       562 
          EPHA2_HUMAN   523 EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK 563
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains 2k9yA00 A:523-563 Single helix bin        CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
           Transcript 1 (1) 1.8   --------------------------------1.1 Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.9b  PDB: A:528-561         -- Transcript 1 (2)
                 2k9y A 523 EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK 563
                                   532       542       552       562 

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with EPHA2_HUMAN | P29317 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:41
                                   532       542       552       562 
          EPHA2_HUMAN   523 EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK 563
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
           Transcript 1 (1) 1.8   --------------------------------1.1 Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.9b  PDB: B:528-561         -- Transcript 1 (2)
                 2k9y B 523 EFQTLSPEGSGNLAVIGGVAVGVVLLLVLAGVGFFIHRRRK 563
                                   532       542       552       562 

   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 2K9Y)

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2K9Y)

(-) Gene Ontology  (62, 62)

NMR Structure(hide GO term definitions)
Chain A,B   (EPHA2_HUMAN | P29317)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005003    ephrin receptor activity    Combining with an ephrin to initiate a change in cell activity.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    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:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0048320    axial mesoderm formation    The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0001568    blood vessel development    The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
    GO:0046849    bone remodeling    The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis.
    GO:0060444    branching involved in mammary gland duct morphogenesis    The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0070309    lens fiber cell morphogenesis    The process in which the structures of a lens fiber cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a lens fiber cell. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.
    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: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:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0021915    neural tube development    The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0060035    notochord cell development    The process whose specific outcome is the progression of a notochord cell over time, from its formation to its mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0014028    notochord formation    The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column.
    GO:0048570    notochord morphogenesis    The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0030316    osteoclast differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0090004    positive regulation of establishment of protein localization to plasma membrane    Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0036342    post-anal tail morphogenesis    The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance.
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0070372    regulation of ERK1 and ERK2 cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0043535    regulation of blood vessel endothelial cell migration    Any process that modulates the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0033628    regulation of cell adhesion mediated by integrin    Any process that modulates the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0010591    regulation of lamellipodium assembly    Any process that modulates the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0070848    response to growth factor    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 growth factor stimulus.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
    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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0031258    lamellipodium membrane    The portion of the plasma membrane surrounding a lamellipodium.
    GO:0031256    leading edge membrane    The portion of the plasma membrane surrounding the leading edge of a motile cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA2_HUMAN | P293171mqb 2e8n 2kso 2x10 2x11 3c8x 3czu 3fl7 3hei 3hpn 3kka 3mbw 3mx0 3skj 4p2k 4pdo 4trl 5ek7 5i9u 5i9v 5i9w 5i9x 5i9y 5i9z 5ia0 5ia1 5ia2 5ia3 5ia4 5ia5 5njz 5nk0 5nk1 5nk2 5nk3 5nk4 5nk5 5nk6 5nk7 5nk8 5nk9 5nka 5nkb 5nkc 5nkd 5nke 5nkf 5nkg 5nkh 5nki

(-) Related Entries Specified in the PDB File

2k1k EPHA1 PH 4.3
2k1l EPHA1 PH 6.3 RELATED ID: 16005 RELATED DB: BMRB