3CD4 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Title :   REFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4

Authors :   T. P. J. Garrett, J. Wang, Y. Yan, S. C. Harrison

Date :   30 Jul 92 (Deposition) - 31 Oct 93 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   T-Cell Surface Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. P. J. Garrett, J. Wang, Y. Yan, J. Liu, S. C. Harrison
Refinement And Analysis Of The Structure Of The First Two Domains Of Human Cd4
J. Mol. Biol. V. 234 763 1993
PubMed-ID: 8254672 | Reference-DOI: 10.1006/JMBI.1993.1625
(for further references see the PDB file header)

Molecule 1 - T CELL SURFACE GLYCOPROTEIN CD4
	Chains	:	A
	Engineered	:	YES
	Organ	:	OVARY
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3CD4)

(no "Site" information available for 3CD4)

Asymmetric Unit

No.	Residues
1	A:16	-	A:84
2	A:130	-	A:159

(no "Cis Peptide Bond" information available for 3CD4)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	A	K	166	E

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023459	K	191	E	CD4_HUMAN	Polymorphism	28917504	A	K	166	E

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

(no "PROSITE Motif" information available for 3CD4)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000011653	1	ENSE00001303311	chr12:6898651-6898828	178	CD4_HUMAN	-	0	0	-	-
1.2	ENST00000011653	2	ENSE00000866954	chr12:6909238-6909353	116	CD4_HUMAN	1-17	17	0	-	-
1.3	ENST00000011653	3	ENSE00000716042	chr12:6909473-6909637	165	CD4_HUMAN	17-72	56	1	A:1-47	47
1.4	ENST00000011653	4	ENSE00000716044	chr12:6923308-6923466	159	CD4_HUMAN	72-125	54	1	A:47-100	54
1.5	ENST00000011653	5	ENSE00000716046	chr12:6923925-6924158	234	CD4_HUMAN	125-203	79	1	A:100-178	79
1.6b	ENST00000011653	6b	ENSE00000716048	chr12:6925222-6925569	348	CD4_HUMAN	203-319	117	1	A:178-178	1
1.7	ENST00000011653	7	ENSE00000716051	chr12:6926296-6926496	201	CD4_HUMAN	319-386	68	0	-	-
1.8	ENST00000011653	8	ENSE00000716053	chr12:6927587-6927708	122	CD4_HUMAN	386-426	41	0	-	-
1.9	ENST00000011653	9	ENSE00000716057	chr12:6928013-6928080	68	CD4_HUMAN	427-449	23	0	-	-
1.10	ENST00000011653	10	ENSE00001182623	chr12:6928465-6929976	1512	CD4_HUMAN	449-458	10	0	-	-

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 A from PDB  Type:PROTEIN  Length:178
 aligned with CD4_HUMAN | P01730 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:178
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195        
            CD4_HUMAN    26 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA 203
               SCOP domains d3cd4a1 A:1-97 CD4 V-set domains                                                                 d3cd4a2 A:98-178 CD4 C2-set domains                                               SCOP domains
               CATH domains 3cd4A01 A:1-98 Immunoglobulins                                                                    3cd4A02 A:99-173 Immunoglobulins                                           ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee..........eeeee....eeeeee..eeee.......eeeehhhhhhheeeeeeee.......eeeeeee..eeeeeeeeeeeeeee....eee..eeeeeee.......eeeee......eee.eeeee........eeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-47 UniProt: 17-72           ----------------------------------------------------Exon 1.5  PDB: A:100-178 UniProt: 125-203                                       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4  PDB: A:47-100 UniProt: 72-125               -----------------------------------------------------------------------------1 Transcript 1 (2)
                 3cd4 A   1 KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLA 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C2 set domains (47)

Protein domain: CD4 C2-set domains (31)

Human (Homo sapiens) [TaxId: 9606] (30)

d3cd4a2

A:98-178

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: CD4 V-set domains (31)

Human (Homo sapiens) [TaxId: 9606] (30)

d3cd4a1

A:1-97

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	3cd4A01	A:1-98
1b	3cd4A02	A:99-173

(no "Pfam Domain" information available for 3CD4)

Asymmetric Unit(hide GO term definitions)

Chain A (CD4_HUMAN | P01730)

molecular function
	GO:0042289	MHC class II protein binding	Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0015026	coreceptor activity	Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0005201	extracellular matrix structural constituent	The action of a molecule that contributes to the structural integrity of the extracellular matrix.
	GO:0019865	immunoglobulin binding	Interacting selectively and non-covalently with an immunoglobulin.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:1990782	protein tyrosine kinase binding	Interacting selectively and non-covalently with protein tyrosine kinase.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045058	T cell selection	The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	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:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0001816	cytokine production	The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0030260	entry into host cell	The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0007167	enzyme linked receptor protein signaling pathway	Any 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 catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0035397	helper T cell enhancement of adaptive immune response	Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0006948	induction by virus of host cell-cell fusion	The process of syncytia-forming cell-cell fusion, caused by a virus.
	GO:0032507	maintenance of protein location in cell	Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
	GO:0050870	positive regulation of T cell activation	Any process that activates or increases the frequency, rate or extent of T cell activation.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0010524	positive regulation of calcium ion transport into cytosol	Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components.
	GO:0050850	positive regulation of calcium-mediated signaling	Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
	GO:0045086	positive regulation of interleukin-2 biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0050863	regulation of T cell activation	Any process that modulates the frequency, rate or extent of T cell activation.
	GO:0050690	regulation of defense response to virus by virus	Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0033280	response to vitamin D	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 vitamin D stimulus.
	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: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: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:0042101	T cell receptor complex	A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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: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: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.

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(no "Ligands, Modified Residues, Ions" information available for 3cd4)

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(no "Sites" information available for 3cd4)

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(no "Cis Peptide Bonds" information available for 3cd4)

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	3cd4
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(no "Related Entries Specified in the PDB File" available for 3CD4)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (4, 4)

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