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- PDB-6y23: DDR1 kinase autoinhibited by its juxtamembrane region -

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Basic information

Entry
Database: PDB / ID: 6y23
TitleDDR1 kinase autoinhibited by its juxtamembrane region
ComponentsEpithelial discoidin domain-containing receptor 1
KeywordsTRANSFERASE / Kinase / Collagen / Cell Signalling
Function / homology
Function and homology information


protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / collagen binding / lactation / embryo implantation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / receptor protein-tyrosine kinase / positive regulation of neuron projection development / cell population proliferation / protein autophosphorylation / receptor complex / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsSammon, D. / Hohenester, E. / Leitinger, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Two-step release of kinase autoinhibition in discoidin domain receptor 1.
Authors: Sammon, D. / Hohenester, E. / Leitinger, B.
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: Epithelial discoidin domain-containing receptor 1
B: Epithelial discoidin domain-containing receptor 1
C: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,90611
Polymers117,1373
Non-polymers7698
Water72140
1
A: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5266
Polymers39,0461
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1422
Polymers39,0461
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2383
Polymers39,0461
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.307, 105.307, 406.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Epithelial discoidin domain-containing receptor 1 / Epithelial discoidin domain receptor 1 / CD167 antigen-like family member A / Cell adhesion kinase ...Epithelial discoidin domain receptor 1 / CD167 antigen-like family member A / Cell adhesion kinase / Discoidin receptor tyrosine kinase / HGK2 / Mammary carcinoma kinase 10 / MCK-10 / Protein-tyrosine kinase 3A / Protein-tyrosine kinase RTK-6 / TRK E / Tyrosine kinase DDR / Tyrosine-protein kinase CAK


Mass: 39045.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Vector derived GP at N-terminus, Y569F and Y586F mutations
Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 9.5 mg/ml protein in 20 mM HEPES pH 7.5, 200 mM NaCl, 1 mM TCEP. Precipitant: 100 mM Tris pH 8.0, 1.5 M ammonium sulphate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.58→58.13 Å / Num. obs: 43468 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.128 / Net I/σ(I): 6.5
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 20.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2087 / CC1/2: 0.443 / Rpim(I) all: 1.129 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3769refinement
PHENIX1.18rc1_3769refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bvw

5bvw


Resolution: 2.58→54.42 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7489
RfactorNum. reflection% reflection
Rfree0.2701 2174 5.01 %
Rwork0.2252 --
obs0.2275 43355 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.65 Å2
Refinement stepCycle: LAST / Resolution: 2.58→54.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7179 0 40 40 7259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277374
X-RAY DIFFRACTIONf_angle_d0.53669999
X-RAY DIFFRACTIONf_chiral_restr0.0391093
X-RAY DIFFRACTIONf_plane_restr0.00411299
X-RAY DIFFRACTIONf_dihedral_angle_d14.64382716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.630.33771290.30962488X-RAY DIFFRACTION99.17
2.63-2.70.34821110.29932528X-RAY DIFFRACTION99.96
2.7-2.760.33841170.29812537X-RAY DIFFRACTION99.96
2.76-2.840.32171330.27842500X-RAY DIFFRACTION99.96
2.84-2.920.29751320.27622531X-RAY DIFFRACTION99.96
2.92-3.020.30751440.26552509X-RAY DIFFRACTION100
3.02-3.120.31181250.25662535X-RAY DIFFRACTION99.89
3.12-3.250.32051480.2382520X-RAY DIFFRACTION100
3.25-3.40.24391420.23252579X-RAY DIFFRACTION100
3.4-3.580.26231280.21252541X-RAY DIFFRACTION99.96
3.58-3.80.25381400.20362561X-RAY DIFFRACTION99.93
3.8-4.090.26661240.20142593X-RAY DIFFRACTION99.93
4.09-4.50.21671590.17292567X-RAY DIFFRACTION99.93
4.5-5.160.24421410.1912636X-RAY DIFFRACTION99.93
5.16-6.490.27141450.21992671X-RAY DIFFRACTION99.75
6.49-54.420.25981560.22722885X-RAY DIFFRACTION99.48

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