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Title :   COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

Authors :   G. V. Louie, W. Yang, M. E. Bowman, S. Choe

Date :   18 Nov 97 (Deposition) - 25 Feb 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : R,T
Biol. Unit 1: R,T  (2x)

Keywords :   Complex (Toxin-Growth Factor), Diphtheria Toxin, Receptor, Heparin- Binding Epidermal Growth Factor, Epidermal Growth Factor, Complex (Toxin-Growth Factor) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. V. Louie, W. Yang, M. E. Bowman, S. Choe
Crystal Structure Of The Complex Of Diphtheria Toxin With A Extracellular Fragment Of Its Receptor.
Mol. Cell V. 1 67 1997
PubMed-ID: 9659904 | Reference-DOI: 10.1016/S1097-2765(00)80008-8

Molecule 1 - DIPHTHERIA TOXIN
	Cellular Location	:	EXTRACELLULAR
	Chains	:	T
	EC Number	:	2.4.2.36
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Synonym	:	DT
	Variant	:	LYSOGENIZED BY THE CORYNEPHAGE BETA

Molecule 2 - HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
	Cellular Location	:	MEMBRANE-ANCHORED OR EXTRACELLULARLY-RELEASED
	Chains	:	R
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HBEGF

		1	2
Asymmetric Unit	:	R	T
Biological Unit 1 (2x)	:	R	T

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1XDT)

Asymmetric Unit

No.	Residues
1	R:108	-	R:121
2	R:116	-	R:132
3	R:134	-	R:143
4	T:186	-	T:201
5	T:461	-	T:471

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

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

Asymmetric Unit (2, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_1	PS00022	EGF-like domain signature 1.	HBEGF_HUMAN	132-143	1	R:132-143
2	EGF_2	PS01186	EGF-like domain signature 2.	HBEGF_HUMAN	132-143	1	R:132-143

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_1	PS00022	EGF-like domain signature 1.	HBEGF_HUMAN	132-143	2	R:132-143
2	EGF_2	PS01186	EGF-like domain signature 2.	HBEGF_HUMAN	132-143	2	R:132-143

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000230990	1a	ENSE00002023958	chr5:139726216-139725868	349	HBEGF_HUMAN	1-16	16	0	-	-
1.2	ENST00000230990	2	ENSE00000764836	chr5:139725669-139725496	174	HBEGF_HUMAN	16-74	59	0	-	-
1.3b	ENST00000230990	3b	ENSE00000764835	chr5:139722397-139722220	178	HBEGF_HUMAN	74-133	60	1	R:107-133	27
1.4b	ENST00000230990	4b	ENSE00000764833	chr5:139715612-139715457	156	HBEGF_HUMAN	133-185	53	1	R:133-147	15
1.5b	ENST00000230990	5b	ENSE00000814136	chr5:139714333-139714243	91	HBEGF_HUMAN	185-208	24	0	-	-
1.6c	ENST00000230990	6c	ENSE00001376016	chr5:139713865-139712428	1438	HBEGF_HUMAN	-	0	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 R from PDB  Type:PROTEIN  Length:41
 aligned with HBEGF_HUMAN | Q99075 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:41
                                   116       126       136       146 
          HBEGF_HUMAN   107 PCLRKYKDFCIHGECKYVKELRAPSCICHPGYHGERCHGLS 147
               SCOP domains d1xdtr_ R:                                SCOP domains
               CATH domains 1xdtR00 R:107-147 Laminin                 CATH domains
               Pfam domains -EGF-1xdtR01 R:108-142              ----- Pfam domains
         Sec.struct. author ............eee...hhh....eee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------EGF_2       ---- PROSITE (1)
                PROSITE (2) -------------------------EGF_1       ---- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: R:107-133  -------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.4b       Transcript 1 (2)
                 1xdt R 107 PCLRKYKDFCIHGECKYVKELRAPSCICHPGYHGERCHGLS 147
                                   116       126       136       146

Chain T from PDB  Type:PROTEIN  Length:518
 aligned with DTX_CORBE | P00588 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:535
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562     
            DTX_CORBE    33 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 567
               SCOP domains d1xdtt2 T:1-188 Diphtheria toxin, N-te      rminal domain                                                                                                                                              d1xdtt3 T:200-380 Diphtheria toxin, middle domain                                                                                                                                    d1xdtt1 T:381-535 Diphtheria toxin, C-terminal domain                                                                                                       SCOP domains
               CATH domains 1xdtT01 T:1-187 Diphtheria Toxin, doma      in 1                                                                                                                                           -           1xdtT02 T:200-379 Diphtheria toxin, middle domain                                                                                                                                   1xdtT03 T:380-533  [code=2.60.40.700, no name defined]                                                                                                    -- CATH domains
               Pfam domains Diphtheria_C-1xdtT01 T:1-187                                                                                                                                                               -           Diphtheria_T-1xdtT03 T:200-379                                                                                                                                                      -Diphtheria_R-1xdtT02 T:381-534                                                                                                                            - Pfam domains
         Sec.struct. author ...........eeee..eeeeee....hhhhhh.....------........eeee..hhhhhhhh............eeeeeee..eeeeee.....hhhhhhh........hhhh...hhhhhh......eeeeeee.......eeeee...hhhheeeeeeee.........hhhhhhhhhh...-----------......hhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhh...........hhhhhhhhhhhhhhhhhhhhhh......hhhh.hhhhhhhhhhhhhhhhhh............eee..eeeee..hhhheee....eeeeeeeeeee........eeeee.............eeee..eeeeeeeee....eeeeee...........eeeeeeeee..............eeeee..eeee..eeee.eeeee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xdt T   1 GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKP------NYDDDWKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACAG-----------SCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS 535
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530     
                                                                38     45                                                                                                                                            188         200

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ADP-ribosyl (56)

Family: Diphtheria_C (4)

Corynephage beta (4)

Diphtheria_C-1xdtT01

T:1-187

Clan: EGF (60)

Family: EGF (31)

Homo sapiens (Human) (25)

EGF-1xdtR01

R:108-142

Clan: no clan defined [family: Diphtheria_R] (4)

Family: Diphtheria_R (4)

Corynephage beta (4)

Diphtheria_R-1xdtT02

T:381-534

Clan: no clan defined [family: Diphtheria_T] (4)

Family: Diphtheria_T (4)

Corynephage beta (4)

Diphtheria_T-1xdtT03

T:200-379

Asymmetric Unit(hide GO term definitions)

Chain R (HBEGF_HUMAN | Q99075)

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: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:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	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:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
biological process
	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: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:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	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:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
	GO:0051545	negative regulation of elastin biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of elastin.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0051549	positive regulation of keratinocyte migration	Any process that activates or increases the frequency, rate or extent of keratinocyte migration.
	GO:0051897	positive regulation of protein kinase B signaling	Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
	GO:0048661	positive regulation of smooth muscle cell proliferation	Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
	GO:0090303	positive regulation of wound healing	Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:2000145	regulation of cell motility	Any process that modulates the frequency, rate or extent of cell motility.
	GO:0008016	regulation of heart contraction	Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
	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: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:0035313	wound healing, spreading of epidermal cells	The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	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: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: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.

Chain T (DTX_CORBE | P00588)

molecular function
	GO:0047286	NAD+-diphthamide ADP-ribosyltransferase activity	Catalysis of the reaction: peptide diphthamide + NAD+ = peptide N-(ADP-D-ribosyl)diphthamide + niacinamide.
	GO:0008320	protein transmembrane transporter activity	Enables the transfer of a protein from one side of a membrane to the other.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	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:0071806	protein transmembrane transport	The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
cellular component
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	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: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.

Asymmetric Unit
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	HBEGF_HUMAN \| Q99075
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	DTX_CORBE \| P00588	:	1ddt 1dtp 1f0l 1mdt 1sgk 1tox 4ae0 4ae1
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(no "Related Entries Specified in the PDB File" available for 1XDT)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (0, 0)

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