1P69 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR VARIATION IN ADENOVIRUS AFFINITY FOR THE CELLULAR RECEPTOR CAR (P417S MUTANT)

Authors :   J. Howitt, M. C. Bewley, V. Graziano, J. M. Flanagan, P. Freimuth

Date :   29 Apr 03 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Virus, Viral Protein, Viral Protein/Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Howitt, M. C. Bewley, V. Graziano, J. M. Flanagan, P. Freimuth
Structural Basis For Variation In Adenovirus Affinity For The Cellular Coxsackievirus And Adenovirus Receptor.
J. Biol. Chem. V. 278 26208 2003
PubMed-ID: 12716886 | Reference-DOI: 10.1074/JBC.M301492200
(for further references see the PDB file header)

Molecule 1 - FIBER PROTEIN
	Chains	:	A
	Mutation	:	YES
	Organism Scientific	:	HUMAN ADENOVIRUS 12
	Organism Taxid	:	28282

Molecule 2 - COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
	Chains	:	B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	COXSACKIEVIRUS B- ADENOVIRUS RECEPTOR, HCAR, CVB3 BINDING PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1P69)

(no "Site" information available for 1P69)

Asymmetric/Biological Unit

No.	Residues
1	B:43	-	B:122

Asymmetric/Biological Unit

No.	Residues
1	Thr A:480	-	Pro A:481
2	Ala B:127	-	Pro B:128

(no "SAP(SNP)/Variant" information available for 1P69)

(no "PROSITE Motif" information available for 1P69)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000284878	1a	ENSE00001356018	chr21:18884700-18885490	791	CXAR_HUMAN	1-15	15	0	-	-
1.4b	ENST00000284878	4b	ENSE00001370254	chr21:18919345-18919511	167	CXAR_HUMAN	15-70	56	1	B:23-72	50
1.5	ENST00000284878	5	ENSE00001016957	chr21:18924067-18924271	205	CXAR_HUMAN	71-139	69	1	B:73-141	69
1.6	ENST00000284878	6	ENSE00001016954	chr21:18931294-18931449	156	CXAR_HUMAN	139-191	53	1	B:141-146	6
1.7	ENST00000284878	7	ENSE00001016953	chr21:18933020-18933142	123	CXAR_HUMAN	191-232	42	0	-	-
1.8	ENST00000284878	8	ENSE00001016956	chr21:18933656-18933794	139	CXAR_HUMAN	232-278	47	0	-	-
1.9f	ENST00000284878	9f	ENSE00001918181	chr21:18937746-18942418	4673	CXAR_HUMAN	278-365	88	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:185
 aligned with SPIKE_ADE12 | P36711 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:185
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
          SPIKE_ADE12   403 TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
               SCOP domains d1p69a_ A: Adenovirus fiber protein knob domain                                                                                                                                           SCOP domains
               CATH domains 1p69A00 A:403-587 Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................eeeeeeeeee..eeeeeeeeee.hhhhhh......eeeeeeee....................eeee..ee......hhhhh.......hhhhh.hhh.eeeeeee.hhh...eeeeeeee........eeeeeeee.hhhh.........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p69 A 403 TPYDPLTLWTTPDPSPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE 587
                                   412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with CXAR_HUMAN | P78310 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
           CXAR_HUMAN    21 SITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQVIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVKPSGA 144
               SCOP domains d1p69b_ B: Coxsackie virus and adenovirus receptor (Car), domain 1                                                           SCOP domains
               CATH domains 1p69B00 B:23-146 Immunoglobulins                                                                                             CATH domains
               Pfam domains -V-set-1p69B01 B:24-139                                                                                              ------- Pfam domains
         Sec.struct. author ......eeeeee....eee.............eeeeeeeee.......eeeeeee..eee...hhhhh..eee...hhhhh...eee...hhhh.eeeeeeeee..eeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:23-72 UniProt: 15-70            Exon 1.5  PDB: B:73-141 UniProt: 71-139                              ----- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------1.6    Transcript 1 (2)
                 1p69 B  23 GITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQVIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVKPSGA 146
                                    32        42        52        62        72        82        92       102       112       122       132       142

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Homo sapiens (Human) (61)

V-set-1p69B01

B:24-139

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPIKE_ADE12 | P36711)

biological process
	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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Chain B (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.

Asymmetric/Biological Unit
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(no "Ligands, Modified Residues, Ions" information available for 1p69)

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(no "Sites" information available for 1p69)

	Cis Peptide Bonds
		Ala B:127 - Pro B:128	[ RasMol ]
		Thr A:480 - Pro A:481	[ RasMol ]

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	1p69
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	SPIKE_ADE12 \| P36711
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Description

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Ligands, Modified Residues, Ions (0, 0)

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