2KV4 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   EGF

Authors :   H. W. Huang, S. K. Mohan, C. Yu

Date :   08 Mar 10 (Deposition) - 23 Feb 11 (Release) - 23 Feb 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)
NMR Structure *: A  (1x)

Keywords :   Epithermal Growth Factor, Egf-Like Domain, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. W. Huang, S. K. Mohan, C. Yu
The Nmr Solution Structure Of Human Epidermal Growth Factor (Hegf) At Physiological Ph And Its Interactions With Surami
Biochem. Biophys. Res. Commun. V. 402 705 2010
PubMed-ID: 21029725 | Reference-DOI: 10.1016/J.BBRC.2010.10.089

Molecule 1 - EPIDERMAL GROWTH FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ORIGAMI B (DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET-32A
	Expression System Vector Type	:	VECTOR
	Gene	:	EGF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
NMR Structure (10x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KV4)

(no "Site" information available for 2KV4)

NMR Structure

No.	Residues
1	A:6	-	A:20
2	A:14	-	A:31
3	A:33	-	A:42

(no "Cis Peptide Bond" information available for 2KV4)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020971	D	981	E	EGF_HUMAN	Polymorphism	11569086	A	D	11	E

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

NMR Structure * (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020971	D	981	E	EGF_HUMAN	Polymorphism	11569086	A	D	11	E

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

NMR Structure (3, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_2	PS01186	EGF-like domain signature 2.	EGF_HUMAN	339-354 380-395 461-476 765-780 855-868 897-910 1001-1012	1	- - - - - - A:31-42
2	EGF_3	PS50026	EGF-like domain profile.	EGF_HUMAN	356-396 831-869 870-911 912-952 972-1013	1	- - - - A:2-43
3	EGF_1	PS00022	EGF-like domain signature 1.	EGF_HUMAN	1001-1012	1	A:31-42

NMR Structure * (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_2	PS01186	EGF-like domain signature 2.	EGF_HUMAN	339-354 380-395 461-476 765-780 855-868 897-910 1001-1012	1	- - - - - - A:31-42
2	EGF_3	PS50026	EGF-like domain profile.	EGF_HUMAN	356-396 831-869 870-911 912-952 972-1013	1	- - - - A:2-43
3	EGF_1	PS00022	EGF-like domain signature 1.	EGF_HUMAN	1001-1012	1	A:31-42

(no "Exon" information available for 2KV4)

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:53
 aligned with EGF_HUMAN | P01133 from UniProtKB/Swiss-Prot  Length:1207

    Alignment length:53
                                   980       990      1000      1010      1020   
           EGF_HUMAN    971 NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR 1023
               SCOP domains d2kv4a_ A: Epidermal growth factor, EGF               SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----EGF-2kv4A01 A:5-41                   ------------ Pfam domains
         Sec.struct. author .....hhhhhh.......................................... Sec.struct. author
                 SAPs(SNPs) ----------E------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------EGF_2       ----------- PROSITE (1)
                PROSITE (2) -EGF_3  PDB: A:2-43 UniProt: 972-1013      ---------- PROSITE (2)
                PROSITE (3) ------------------------------EGF_1       ----------- PROSITE (3)
                 Transcript ----------------------------------------------------- Transcript
                2kv4 A    1 NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR   53
                                    10        20        30        40        50

Chain A from PDB  Type:PROTEIN  Length:53
 aligned with Q6QBS2_HUMAN | Q6QBS2 from UniProtKB/TrEMBL  Length:53

    Alignment length:53
                                    10        20        30        40        50   
        Q6QBS2_HUMAN      1 NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR   53
               SCOP domains d2kv4a_ A: Epidermal growth factor, EGF               SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----EGF-2kv4A01 A:5-41                   ------------ Pfam domains
         Sec.struct. author .....hhhhhh.......................................... Sec.struct. author
                 SAPs(SNPs) ----------E------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                2kv4 A    1 NSDSECPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWWELR   53
                                    10        20        30        40        50

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: EGF/Laminin (347)

Family: EGF-type module (304)

Protein domain: Epidermal growth factor, EGF (13)

Human (Homo sapiens) [TaxId: 9606] (5)

d2kv4a_

(no "CATH Domain" information available for 2KV4)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EGF (60)

Family: EGF (31)

Homo sapiens (Human) (25)

EGF-2kv4A01

A:5-41

NMR Structure(hide GO term definitions)

Chain A (EGF_HUMAN | P01133)

molecular function
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0042813	Wnt-activated receptor activity	Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity.
	GO:0017147	Wnt-protein binding	Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	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:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0030297	transmembrane receptor protein tyrosine kinase activator activity	Binds to and increases the activity of a transmembrane receptor protein tyrosine kinase.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0038128	ERBB2 signaling pathway	A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
	GO:0070371	ERK1 and ERK2 cascade	An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007262	STAT protein import into nucleus	The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases.
	GO:0044332	Wnt signaling pathway involved in dorsal/ventral axis specification	The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell contributing to the establishment, maintenance and elaboration of the dorsal/ventral axis.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0000186	activation of MAPKK activity	The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
	GO:0007171	activation of transmembrane receptor protein tyrosine kinase activity	Any process that initiates the activity of the inactive transmembrane receptor protein tyrosine kinase activity.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0048754	branching morphogenesis of an epithelial tube	The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
	GO:0060070	canonical Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
	GO:0007173	epidermal growth factor receptor signaling pathway	A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0060749	mammary gland alveolus development	The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
	GO:0090370	negative regulation of cholesterol efflux	Any process that decreases the frequency, rate or extent of cholesterol efflux. Cholesterol efflux is the directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0051048	negative regulation of secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0043388	positive regulation of DNA binding	Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0035413	positive regulation of catenin import into nucleus	Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0021940	positive regulation of cerebellar granule cell precursor proliferation	The process that activates or increases the rate or extent of granule cell precursor proliferation.
	GO:0045741	positive regulation of epidermal growth factor-activated receptor activity	Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity.
	GO:1900127	positive regulation of hyaluronan biosynthetic process	Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.
	GO:0010800	positive regulation of peptidyl-threonine phosphorylation	Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	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:0042327	positive regulation of phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
	GO:2000060	positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of protein ubiquitination involved in ubiquitin-dependent protein catabolic process.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0090279	regulation of calcium ion import	Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
	GO:2000145	regulation of cell motility	Any process that modulates the frequency, rate or extent of cell motility.
	GO:0050730	regulation of peptidyl-tyrosine phosphorylation	Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:2000008	regulation of protein localization to cell surface	Any process that modulates the frequency, rate or extent of protein localization to the cell surface.
	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.
cellular component
	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: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: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:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	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:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.
	GO:0043235	receptor complex	Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

Chain A (Q6QBS2_HUMAN | Q6QBS2)

NMR Structure
	Complete Structure
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(no "Sites" information available for 2kv4)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kv4)

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	2kv4
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	EGF_HUMAN \| P01133	:	1ivo 1jl9 1nql 1p9j 3njp
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(no "Related Entries Specified in the PDB File" available for 2KV4)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

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