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- PDB-1xdt: COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH ... -

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Basic information

Entry
Database: PDB / ID: 1xdt
TitleCOMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
Components
  • DIPHTHERIA TOXIN
  • HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
KeywordsCOMPLEX (TOXIN/GROWTH FACTOR) / COMPLEX (TOXIN-GROWTH FACTOR) / DIPHTHERIA TOXIN / RECEPTOR / HEPARIN-BINDING EPIDERMAL GROWTH FACTOR / EPIDERMAL GROWTH FACTOR / COMPLEX (TOXIN-GROWTH FACTOR) complex
Function / homology
Function and homology information


negative regulation of elastin biosynthetic process / NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / ERBB2-ERBB4 signaling pathway / positive regulation of keratinocyte migration / PI3K events in ERBB4 signaling / wound healing, spreading of epidermal cells / Inhibition of Signaling by Overexpressed EGFR / regulation of heart contraction / EGFR interacts with phospholipase C-gamma ...negative regulation of elastin biosynthetic process / NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / ERBB2-ERBB4 signaling pathway / positive regulation of keratinocyte migration / PI3K events in ERBB4 signaling / wound healing, spreading of epidermal cells / Inhibition of Signaling by Overexpressed EGFR / regulation of heart contraction / EGFR interacts with phospholipase C-gamma / muscle organ development / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Uptake and function of diphtheria toxin / positive regulation of wound healing / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / protein transmembrane transporter activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / SHC1 events in ERBB4 signaling / GAB1 signalosome / Nuclear signaling by ERBB4 / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / nucleotidyltransferase activity / SHC1 events in ERBB2 signaling / cell chemotaxis / EGFR downregulation / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / clathrin-coated endocytic vesicle membrane / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / heparin binding / toxin activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / Extra-nuclear estrogen signaling / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain ...Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Laminin / Laminin / EGF-like domain / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Globin-like / Ribbon / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Diphtheria toxin / Proheparin-binding EGF-like growth factor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLouie, G.V. / Yang, W. / Bowman, M.E. / Choe, S.
CitationJournal: Mol.Cell / Year: 1997
Title: Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor.
Authors: Louie, G.V. / Yang, W. / Bowman, M.E. / Choe, S.
History
DepositionNov 18, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DIPHTHERIA TOXIN
R: HEPARIN-BINDING EPIDERMAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)67,3392
Polymers67,3392
Non-polymers00
Water86548
1
T: DIPHTHERIA TOXIN
R: HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

T: DIPHTHERIA TOXIN
R: HEPARIN-BINDING EPIDERMAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)134,6784
Polymers134,6784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12640 Å2
ΔGint-50 kcal/mol
Surface area43090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.400, 103.700, 127.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsDIPHTHERIA TOXIN MOLECULE HAS THE OPEN CONFORMATION, AND DIMERIZES WITH ANOTHER DIPHTHERIA TOXIN MOLECULE.

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Components

#1: Protein DIPHTHERIA TOXIN / / DT


Mass: 58411.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Variant: LYSOGENIZED BY THE CORYNEPHAGE BETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Protein HEPARIN-BINDING EPIDERMAL GROWTH FACTOR / HBEGF


Mass: 8927.515 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Cellular location: MEMBRANE-ANCHORED OR EXTRACELLULARLY-RELEASED
Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99075
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) GLYCEROL, 22-30% (W/V) ...Details: PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) GLYCEROL, 22-30% (W/V) POLYETHYLENE GLYCOL 3350; AND EQUILIBRATED BY VAPOR DIFFUSION AGAINST PRECIPITANT, vapor diffusion
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-30 mg/mlprotein1drop
20.15 M1dropNaCl
310 mMTris-HCl1drop
422-30 %(w/v)PEG33501reservoir
52.0 M1reservoirNaCl
65 %(v/v)glycerol1reservoir
750 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 54532 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 27.9
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5 / Rsym value: 0.152 / % possible all: 79.2
Reflection shell
*PLUS
% possible obs: 79.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MDT

1mdt


Resolution: 2.65→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 750 4.8 %RANDOM
Rwork0.172 ---
obs0.172 15511 88.5 %-
Displacement parametersBiso mean: 37.9 Å2
Refinement stepCycle: LAST / Resolution: 2.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 0 48 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.451.5
X-RAY DIFFRACTIONx_mcangle_it5.212
X-RAY DIFFRACTIONx_scbond_it5.232
X-RAY DIFFRACTIONx_scangle_it7.352.5
LS refinement shellResolution: 2.65→2.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.367 90 5.2 %
Rwork0.245 1627 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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