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- PDB-8pe9: Complex between DDR1 DS-like domain and PRTH-101 Fab -

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Entry
Database: PDB / ID: 8pe9
TitleComplex between DDR1 DS-like domain and PRTH-101 Fab
Components
  • (PRTH-101 Fab, ...) x 2
  • Epithelial discoidin domain-containing receptor 1
KeywordsIMMUNE SYSTEM / Humanized antibody / DDR1 / collagen / immune exclusion / breast cancer
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: 3.152 Å
AuthorsLiu, J. / Chiang, H. / Xiong, W. / Laurent, V. / Griffiths, S.C. / Duelfer, J. / Deng, H. / Sun, X. / Yin, Y.W. / Li, W. ...Liu, J. / Chiang, H. / Xiong, W. / Laurent, V. / Griffiths, S.C. / Duelfer, J. / Deng, H. / Sun, X. / Yin, Y.W. / Li, W. / Audoly, L.P. / An, Z. / Schuerpf, T. / Li, R. / Zhang, N.
Funding support United States, 4items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP150551 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190561 United States
Welch FoundationAU-0042-20030616 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA246707 United States
CitationJournal: J Immunother Cancer / Year: 2023
Title: A highly selective humanized DDR1 mAb reverses immune exclusion by disrupting collagen fiber alignment in breast cancer.
Authors: Liu, J. / Chiang, H.C. / Xiong, W. / Laurent, V. / Griffiths, S.C. / Dulfer, J. / Deng, H. / Sun, X. / Yin, Y.W. / Li, W. / Audoly, L.P. / An, Z. / Schurpf, T. / Li, R. / Zhang, N.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epithelial discoidin domain-containing receptor 1
H: PRTH-101 Fab, heavy chain
L: PRTH-101 Fab, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07410
Polymers67,0233
Non-polymers1,0517
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-130 kcal/mol
Surface area27110 Å2
Unit cell
Length a, b, c (Å)117.096, 144.45, 52.299
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#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: 20382.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DDR1 DS-like domain, produced via trypsin digestion of DDR1 extracellular domain (recombinantly overexpressed and purified from Expi293F cells using a pcDNA3.4 vector).
Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q08345, receptor protein-tyrosine kinase

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Antibody , 2 types, 2 molecules HL

#2: Antibody PRTH-101 Fab, heavy chain


Mass: 23853.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab from PRTH-101 heavy chain, generated via papain digest of full monoclonal antibody (recombinantly overexpressed and purified from ExpiCHO-S cells using pcDNA3.4 vector).
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.4 / Cell (production host): ExpiCHO-S / Production host: Homo sapiens (human)
#3: Antibody PRTH-101 Fab, light chain


Mass: 22786.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab from PRTH-101 light chain, generated via papain digest of full monoclonal antibody (recombinantly overexpressed and purified from ExpiCHO-S cells using pcDNA3.4 vector).
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.4 / Cell line (production host): ExpiCHO-S / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Details

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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, pH 6.0, 20% (w/v) PEG 6000, 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.152→72.225 Å / Num. obs: 9760 / % possible obs: 85.9 % / Redundancy: 5.97 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.985 / CC1/2 anomalous: 0.011 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.1224 / Rrim(I) all: 0.3038 / AbsDiff over sigma anomalous: 0.817 / Baniso tensor eigenvalue 1: 85.4 Å2 / Baniso tensor eigenvalue 2: 50.7 Å2 / Baniso tensor eigenvalue 3: 103.8 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.559 Å / Aniso diffraction limit 2: 3.109 Å / Aniso diffraction limit 3: 4.028 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 7.05 / Num. measured all: 58265 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 85 / % possible ellipsoidal: 85.9 / % possible ellipsoidal anomalous: 85 / % possible spherical: 61.1 / % possible spherical anomalous: 58.7 / Redundancy anomalous: 3.28 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
10.551-72.2255.550.04826.05270927094884880.9980.0920.02230.05320.89210099.810099.81003.599.8
8.279-10.5515.760.059621.64281328134884880.998-0.0130.02750.0660.8498.997.498.997.498.93.3197.4
7.161-8.2795.320.147410.9259525954884880.9910.0120.07030.16390.82299.59999.59999.52.9799
6.48-7.1615.830.20968.03284628464884880.9780.0120.09480.23080.80999.799.899.799.899.73.2499.8
6.011-6.485.980.27016.65291729174884880.956-0.0650.12080.29680.8621001001001001003.28100
5.64-6.0116.110.28936.44298129814884880.945-0.0740.1270.31680.7521001001001001003.37100
5.344-5.646.320.31146.05307730774874870.9530.0420.13480.340.811001001001001003.42100
5.107-5.3446.230.2657.23304230424884880.9580.070.11620.29020.831001001001001003.42100
4.904-5.1076.330.29216.72309330934894890.9570.0880.12710.31940.7871001001001001003.42100
4.729-4.9046.360.27586.92309530954874870.966-0.0640.11850.30080.76310099.810099.81003.4599.8
4.577-4.7296.280.30366.15306930694894890.948-0.050.13260.33220.82899.599.899.599.899.53.3999.8
4.44-4.5776.290.33745.61306930694884880.9510.050.1460.36850.8799.19999.19999.13.3899
4.318-4.445.740.38454.6279527954874870.902-0.1030.17410.42390.78397.698.297.698.297.63.1598.2
4.198-4.3185.090.44713.74248224824884880.8620.0820.21870.50090.85489.688.189.688.189.62.7188.1
4.09-4.1985.660.56223.32276727674894890.906-0.0010.25490.61890.81489.289.989.289.989.23.0389.9
3.988-4.095.840.61453.04284428444874870.8550.0870.2760.67550.77288.688.788.685.786.73.188.7
3.837-3.9885.750.86271.98280728074884880.788-0.0180.38130.94530.80256.457.556.451.150.33.1157.5
3.739-3.8376.150.85372.17300730074894890.8160.1360.36770.93130.85387.688.687.670.6693.388.6
3.562-3.7396.170.91941.93300930094884880.821-0.0310.39091.00140.80350.953.650.93330.63.4153.6
3.152-3.5626.661.07371.79324832484884880.611-0.0320.44411.16440.81944.647.444.610.18.73.7847.4

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
STARANISO2.3.79data scaling
BUSTER2.11.8refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AG4

4ag4


Resolution: 3.152→72.22 Å / Cor.coef. Fo:Fc: 0.828 / Cor.coef. Fo:Fc free: 0.796 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.779
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 496 -RANDOM
Rwork0.2782 ---
obs0.2798 9760 61 %-
Displacement parametersBiso mean: 68.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.5309 Å20 Å20 Å2
2--5.2089 Å20 Å2
3----7.7397 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 3.152→72.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 57 0 4645
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0044757HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.696467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1586SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes798HARMONIC5
X-RAY DIFFRACTIONt_it4757HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion614SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3201SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.83
X-RAY DIFFRACTIONt_other_torsion14.8
LS refinement shellResolution: 3.152→3.53 Å
RfactorNum. reflection% reflection
Rfree0.576 13 -
Rwork0.3315 --
obs--8.95 %

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