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(-) Description

Title :  KINETIC AND STRUCTURAL ANALYSIS OF COXSACKIEVIRUS B3 RECEPTOR INTERACTIONS AND FORMATION OF THE A-PARTICLE
 
Authors :  L. J. Organtini, A. M. Makhov, J. F. Conway, S. Hafenstein, S. D. Carson
Date :  19 Mar 14  (Deposition) - 09 Apr 14  (Release) - 07 May 14  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.00
Chains :  Asym. Unit :  K
Biol. Unit 1:  K  (60x)
Keywords :  Coxsackievirus B3, Cvb3, Car, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Organtini, A. M. Makhov, J. F. Conway, S. Hafenstein, S. D. Carson
Kinetic And Structural Analysis Of Coxsackievirus B3 Receptor Interactions And Formation Of The A-Particle.
J. Virol. V. 88 5755 2014
PubMed-ID: 24623425  |  Reference-DOI: 10.1128/JVI.00299-14

(-) Compounds

Molecule 1 - COXSACKIE AND ADENOVIRUS RECEPTOR
    ChainsK
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSEE REMARK 999
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit K
Biological Unit 1 (60x)K

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J6N)

(-) Sites  (0, 0)

(no "Site" information available for 3J6N)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1K:41 -K:120
2K:146 -K:223
3K:162 -K:212

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala K:125 -Pro K:126
2Leu K:169 -Pro K:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J6N)

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002848781aENSE00001356018chr21:18884700-18885490791CXAR_HUMAN1-15150--
1.4bENST000002848784bENSE00001370254chr21:18919345-18919511167CXAR_HUMAN15-70561K:25-7046
1.5ENST000002848785ENSE00001016957chr21:18924067-18924271205CXAR_HUMAN71-139691K:71-13969
1.6ENST000002848786ENSE00001016954chr21:18931294-18931449156CXAR_HUMAN139-191531K:139-19153
1.7ENST000002848787ENSE00001016953chr21:18933020-18933142123CXAR_HUMAN191-232421K:191-23242
1.8ENST000002848788ENSE00001016956chr21:18933656-18933794139CXAR_HUMAN232-278471K:232-2332
1.9fENST000002848789fENSE00001918181chr21:18937746-189424184673CXAR_HUMAN278-365880--

(-) Sequences/Alignments

Asymmetric 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 K from PDB  Type:PROTEIN  Length:209
 aligned with CXAR_HUMAN | P78310 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:209
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         
           CXAR_HUMAN    25 PEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQVIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVKPSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISVKNASSEYSGTYSCTVRNRVGSDQCLLRLNVVPPS 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eee..............eeeeeeee.......eeeeeee..eee...hhhhh..eee...hhhhh...eee...hhhh.eeeeeeeee..eeeeeeeeeeee......eeeee........eeeeee........eeeeee.......hhhhhhhh...eeee...hhhhheeeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: K:25-70 UniProt: 15-70        Exon 1.5  PDB: K:71-139 UniProt: 71-139                              ---------------------------------------------------Exon 1.7  PDB: K:191-232 UniProt: 191-232 - Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: K:139-191 UniProt: 139-191            ----------------------------------------1. Transcript 1 (2)
                 3j6n K  25 PEQRIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPSDNQIVDQVIILYSGDKIYDNYYPDLKGRVHFTSNDVKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKFLLTVLVKPSGTRCFVDGSEEIGNDFKLKCEPKEGSLPLQFEWQKLSDSQTMPTPWLAEMTSPVISVKNASSEYSGTYSCTVQNRVGSDQCMLRLDVVPPS 233
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         

   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 3J6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J6N)

(-) Gene Ontology  (52, 52)

Asymmetric Unit(hide GO term definitions)
Chain K   (CXAR_HUMAN | P78310)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0071253    connexin binding    Interacting selectively and non-covalently with a connexin, any of a group of related proteins that assemble to form gap junctions.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0086067    AV node cell to bundle of His cell communication    The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0048739    cardiac muscle fiber development    The process whose specific outcome is the progression of cardiac muscle fiber over time, from its formation to the mature structure.
    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:0045216    cell-cell junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0010669    epithelial structure maintenance    A tissue homeostatic process required for the maintenance of epithelial structure.
    GO:0046629    gamma-delta T cell activation    The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0008354    germ cell migration    The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form.
    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:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0034109    homotypic cell-cell adhesion    The attachment of a cell to a second cell of the identical type via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0070633    transepithelial transport    The directed movement of a substance from one side of an epithelium to the other.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0016327    apicolateral plasma membrane    The apical end of the lateral plasma membrane of epithelial cells.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0014704    intercalated disc    A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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: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
        CXAR_HUMAN | P783101eaj 1f5w 1jew 1kac 1p69 1p6a 1rsf 2j12 2j1k 2npl 2w9l 2wbw 3j6l 3j6m 3j6o

(-) Related Entries Specified in the PDB File

3j6l 3j6m 3j6o