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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN EPIDERMAL GROWTH FACTOR
 
Authors :  H. S. Lu, J. J. Chai, M. Li, B. R. Huang, C. H. He, R. C. Bi
Date :  16 Jul 01  (Deposition) - 24 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimerization, Growth Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Lu, J. J. Chai, M. Li, B. R. Huang, C. H. He, R. C. Bi
Crystal Structure Of Human Epidermal Growth Factor And Its Dimerization
J. Biol. Chem. V. 276 34913 2001
PubMed-ID: 11438527  |  Reference-DOI: 10.1074/JBC.M102874200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-51
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EGF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1JL9)

(-) Sites  (0, 0)

(no "Site" information available for 1JL9)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:20
2A:14 -A:31
3A:33 -A:42
4B:6 -B:20
5B:14 -B:31
6B:33 -B:42

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JL9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020971D981EEGF_HUMANPolymorphism11569086A/BD11E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_2PS01186 EGF-like domain signature 2.EGF_HUMAN339-354
380-395
461-476
765-780
855-868
897-910
1001-1012
 		  2-
-
-
-
-
-
A:31-42
B:31-42
2EGF_1PS00022 EGF-like domain signature 1.EGF_HUMAN1001-1012
 		  2A:31-42
B:31-42

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002651711bENSE00001081340chr4:110834047-110834618572EGF_HUMAN1-43430--
1.2bENST000002651712bENSE00000736651chr4:110862102-110862301200EGF_HUMAN43-109670--
1.3aENST000002651713aENSE00000736652chr4:110864410-110864591182EGF_HUMAN110-170610--
1.4bENST000002651714bENSE00000736653chr4:110864998-110865225228EGF_HUMAN170-246770--
1.5ENST000002651715ENSE00000736654chr4:110866229-110866431203EGF_HUMAN246-314690--
1.6bENST000002651716bENSE00000736655chr4:110880468-110880593126EGF_HUMAN314-356430--
1.7ENST000002651717ENSE00000736656chr4:110882023-110882145123EGF_HUMAN356-397420--
1.8ENST000002651718ENSE00000736657chr4:110883019-110883141123EGF_HUMAN397-438420--
1.9bENST000002651719bENSE00000736658chr4:110884329-110884454126EGF_HUMAN438-480430--
1.10ENST0000026517110ENSE00000736659chr4:110885557-110885693137EGF_HUMAN480-525460--
1.11bENST0000026517111bENSE00000736660chr4:110890127-110890275149EGF_HUMAN526-575500--
1.12ENST0000026517112ENSE00000736662chr4:110895859-110895963105EGF_HUMAN575-610360--
1.13bENST0000026517113bENSE00000736665chr4:110897168-110897391224EGF_HUMAN610-685760--
1.14ENST0000026517114ENSE00000736668chr4:110901128-110901295168EGF_HUMAN685-741570--
1.15cENST0000026517115cENSE00000736670chr4:110901982-110902131150EGF_HUMAN741-791510--
1.16ENST0000026517116ENSE00000736672chr4:110904578-110904697120EGF_HUMAN791-831410--
1.17bENST0000026517117bENSE00000736674chr4:110908900-110909016117EGF_HUMAN831-870400--
1.18ENST0000026517118ENSE00000736676chr4:110909740-110909865126EGF_HUMAN870-912430--
1.19ENST0000026517119ENSE00000736679chr4:110914403-110914525123EGF_HUMAN912-953420--
1.20ENST0000026517120ENSE00000736682chr4:110915889-110916036148EGF_HUMAN953-1002502A:6-32
B:6-32		27
27
1.21ENST0000026517121ENSE00000736686chr4:110920835-110921002168EGF_HUMAN1002-1058572A:32-47
B:32-50		16
19
1.22ENST0000026517122ENSE00000736691chr4:110925661-110925778118EGF_HUMAN1058-1097400--
1.23ENST0000026517123ENSE00000736696chr4:110929308-11092938679EGF_HUMAN1098-1124270--
1.24dENST0000026517124dENSE00001081339chr4:110932358-1109334221065EGF_HUMAN1124-1207840--

(-) Sequences/Alignments

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
(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:42
 aligned with EGF_HUMAN | P01133 from UniProtKB/Swiss-Prot  Length:1207

    Alignment length:42
                                   985       995      1005      1015  
           EGF_HUMAN    976 CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDL 1017
               SCOP domains d1jl9a_ A: Epidermal growth factor, EGF    SCOP domains
               CATH domains 1jl9A00 A:6-47 Laminin                     CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeehhhheeeee....ee.....ee.. Sec.struct. author
                 SAPs(SNPs) -----E------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------EGF_2       ----- PROSITE (1)
                PROSITE (2) -------------------------EGF_1       ----- PROSITE (2)
           Transcript 1 (1) Exon 1.20  PDB: A:6-32     --------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.21        Transcript 1 (2)
                1jl9 A    6 CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDL   47
                                    15        25        35        45  


Chain B from PDB  Type:PROTEIN  Length:45
 aligned with EGF_HUMAN | P01133 from UniProtKB/Swiss-Prot  Length:1207

    Alignment length:45
                                   985       995      1005      1015     
           EGF_HUMAN    976 CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWW 1020
               SCOP domains d1jl9b_ B: Epidermal growth factor, EGF       SCOP domains
               CATH domains 1jl9B00 B:6-50 Laminin                        CATH domains
           Pfam domains (1) EGF-1jl9B01 B:6-41                  --------- Pfam domains (1)
           Pfam domains (2) EGF-1jl9B02 B:6-41                  --------- Pfam domains (2)
         Sec.struct. author .............eeeeehhhheeeee....ee.....ee..... Sec.struct. author
                 SAPs(SNPs) -----E--------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------EGF_2       -------- PROSITE (1)
                PROSITE (2) -------------------------EGF_1       -------- PROSITE (2)
           Transcript 1 (1) Exon 1.20  PDB: B:6-32     ------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.21           Transcript 1 (2)
                1jl9 B    6 CPLSHDGYCLHDGVCMYIEALDKYACNCVVGYIGERCQYRDLKWW   50
                                    15        25        35        45
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: EGF (60)

(-) Gene Ontology  (60, 60)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGF_HUMAN | P01133: 1ivo 1nql 1p9j 2kv4 3njp

(-) Related Entries Specified in the PDB File

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