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- PDB-7wg3: Structural basis of interleukin-17B receptor in complex with a ne... -

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Basic information

Entry
Database: PDB / ID: 7wg3
TitleStructural basis of interleukin-17B receptor in complex with a neutralizing antibody D9 for guiding humanization and affinity maturation for cancer therapy
Components
  • Heavy chain of D9 Fab
  • IL17RB protein
  • Light chain of D9 Fab
KeywordsIMMUNE SYSTEM / IL-17B / IL17RB / antibody / complex / interleukin-17 B receptor / pancreatic cancer / cancer target therapy / antibody engineering
Function / homology
Function and homology information


interleukin-17 receptor activity / plasma membrane
Similarity search - Function
Interleukin-17 receptor A/B, fibronectin-III-like domain 2 / Interleukin-17 receptor A/B, fibronectin-III-like domain 1 / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin 17 receptor D / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain ...Interleukin-17 receptor A/B, fibronectin-III-like domain 2 / Interleukin-17 receptor A/B, fibronectin-III-like domain 1 / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin-17 receptor A/B, FnIII-like domain 1 superfamily / Interleukin-17 receptor A/B, FnIII-like domain 2 superfamily / Interleukin-17 receptor, fibronectin-III-like domain 1 / Interleukin 17 receptor D / Interleukin-17 receptor-like / SEFIR domain / SEFIR domain / SEFIR domain profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLee, W.H. / Chen, X.R. / Liu, I.J. / Lee, J.H. / Hu, C.M. / Wu, H.C. / Wang, S.K. / Lee, W.H. / Ma, C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2022
Title: Structural basis of interleukin-17B receptor in complex with a neutralizing antibody for guiding humanization and affinity maturation.
Authors: Lee, W.H. / Chen, X. / Liu, I.J. / Lee, J.H. / Hu, C.M. / Wu, H.C. / Wang, S.K. / Lee, W.H. / Ma, C.
History
DepositionDec 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of D9 Fab
B: Light chain of D9 Fab
C: Light chain of D9 Fab
D: Light chain of D9 Fab
E: Heavy chain of D9 Fab
F: Heavy chain of D9 Fab
G: Heavy chain of D9 Fab
H: Heavy chain of D9 Fab
I: IL17RB protein
J: IL17RB protein
K: IL17RB protein
L: IL17RB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,74632
Polymers299,78012
Non-polymers5,96620
Water18,7181039
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.020, 195.030, 98.840
Angle α, β, γ (deg.)90.000, 98.130, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and (resid 1 through 79 or resid 81...
d_3ens_1(chain "C" and ((resid 1 and (name N or name...
d_4ens_1(chain "D" and ((resid 1 and (name N or name...
d_1ens_2(chain "E" and (resid 1 through 42 or (resid 43...
d_2ens_2(chain "F" and ((resid 1 and (name N or name...
d_3ens_2(chain "G" and ((resid 1 and (name N or name...
d_4ens_2(chain "H" and (resid 1 through 4 or (resid 5...
d_1ens_3(chain "I" and (resid 1 or (resid 2 and (name...
d_2ens_3(chain "J" and (resid 1 or (resid 2 and (name...
d_3ens_3(chain "K" and (resid 1 or (resid 2 and (name...
d_4ens_3(chain "L" and (resid 1 through 19 or (resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNALAA1 - 79
d_12ens_1ASPLEUA81 - 124
d_13ens_1SERCYSA126 - 213
d_21ens_1GLNALAB1 - 79
d_22ens_1ASPLEUB81 - 124
d_23ens_1SERCYSB126 - 213
d_31ens_1GLNALAC1 - 79
d_32ens_1ASPLEUC81 - 124
d_33ens_1SERCYSC126 - 213
d_41ens_1GLNALAD1 - 79
d_42ens_1ASPLEUD81 - 124
d_43ens_1SERCYSD126 - 213
d_11ens_2GLUGLYE1 - 66
d_12ens_2ALASERE68 - 133
d_13ens_2GLYASPE137 - 220
d_21ens_2GLUGLYF1 - 66
d_22ens_2ALASERF68 - 133
d_23ens_2GLYASPF137 - 220
d_31ens_2GLUGLYG1 - 66
d_32ens_2ALASERG68 - 133
d_33ens_2GLYASPG137 - 220
d_41ens_2GLUGLYH1 - 66
d_42ens_2ALASERH68 - 133
d_43ens_2GLYASPH137 - 220
d_11ens_3PROLEUI1 - 55
d_12ens_3SERSERI60 - 75
d_13ens_3TYRTHRI80 - 93
d_14ens_3ARGASNI96 - 126
d_15ens_3PROSERI130 - 199
d_16ens_3VALPROI201 - 248
d_21ens_3PROLEUT1 - 55
d_22ens_3SERSERT60 - 75
d_23ens_3TYRTHRT80 - 93
d_24ens_3ARGSERT96 - 196
d_25ens_3VALPROT198 - 245

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999091434104, -0.0426133181522, -0.000641416815525), (-0.0426132399364, -0.999091634197, 0.000135124892084), (-0.000646592294441, -0.000107669273556, -0.999999785163)-31.1600293565, 99.6941706493, 50.0451357664
2given(0.956368731866, 0.166535852571, -0.240051366415), (-0.132235481787, 0.979396833407, 0.152629027609), (0.260523753362, -0.114226321489, 0.958686456258)-31.7561697108, -2.48190455963, -1.83182694981
3given(0.952912852558, 0.155663045776, -0.260242409321), (0.130950920545, -0.985284184422, -0.109849589601), (-0.273512251714, 0.070598102714, -0.959274181898)6.79331334434, 100.882996816, 53.4961931697
4given(0.955805367117, -0.195810795805, 0.219303972688), (-0.159716204914, -0.972089204955, -0.171852586532), (0.246833616184, 0.12923122632, -0.9604022366)6.23037100157, 97.0950404353, 42.0178508196
5given(0.999568851475, -0.0290463822204, 0.00429171775116), (-0.028991979894, -0.999504740851, -0.0122367527997), (0.00464502563764, 0.012107051547, -0.999915917985)34.1684423384, 99.1058746833, 49.3426113635
6given(0.943911375941, -0.197830354089, 0.264375614175), (0.172260496062, 0.978093738576, 0.116871553656), (-0.281704873699, -0.0647749145758, 0.95731216151)42.9803233012, 2.96565241442, 2.84977335438
7given(0.986426267145, -0.120811093265, -0.111211057141), (-0.123011665069, -0.992318523363, -0.0131178675183), (-0.108772008088, 0.0266200664019, -0.993710230561)5.6250855095, 102.032974997, 52.1963795366
8given(0.991004991039, 0.121845816881, 0.0553417080008), (-0.120381932942, 0.992301952562, -0.0290693165105), (-0.0584576595237, 0.0221456959666, 0.998044222564)-41.332275526, 0.827537728768, -0.723832424071
9given(0.994538818048, -0.1043399558, 0.00239019216464), (-0.104118154393, -0.99348574302, -0.0463194164671), (0.00720758770548, 0.045817595309, -0.998923820238)-30.7752919744, 100.635363775, 46.8712745522

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Components

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Antibody , 2 types, 8 molecules ABCDEFGH

#1: Antibody
Light chain of D9 Fab


Mass: 23269.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma cell / Plasmid: IgK1 / Details (production host): A gift from Dr. Tse Wen Chang / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody
Heavy chain of D9 Fab


Mass: 23499.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Details (production host): A gift from Tse Wen Chang / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 1043 molecules IJKL

#3: Protein
IL17RB protein / Interleukin 17 receptor B


Mass: 28176.115 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IL17RB / Production host: Homo sapiens (human) / References: UniProt: A3KN55
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1039 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 20 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}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.: 18 / 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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Details

Has ligand of interestN
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.01 % / Description: Twinned blade
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.1M Bicine, pH 8.2, 17% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: Oxford Instrument CryoJet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.007 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 18, 2018
Details: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.19→38.03 Å / Num. obs: 134260 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 36.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05615 / Rrim(I) all: 0.07941 / Net I/σ(I): 7.08
Reflection shellResolution: 2.19→2.268 Å / Rmerge(I) obs: 0.508 / Num. unique obs: 13343 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJG, 4KUZ, 3JVF

4hjg

4kuz

3jvf


Resolution: 2.19→38.03 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 6853 5.11 %
Rwork0.1931 127371 -
obs0.1954 134224 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.47 Å2
Refinement stepCycle: LAST / Resolution: 2.19→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20525 0 385 1039 21949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821441
X-RAY DIFFRACTIONf_angle_d1.080729197
X-RAY DIFFRACTIONf_chiral_restr0.06573404
X-RAY DIFFRACTIONf_plane_restr0.00833667
X-RAY DIFFRACTIONf_dihedral_angle_d13.31097685
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.891694596232
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.657463923702
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.643631799088
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS1.93536839225
ens_2d_3EX-RAY DIFFRACTIONTorsion NCS1.20151683848
ens_2d_4EX-RAY DIFFRACTIONTorsion NCS1.43563510536
ens_3d_2IX-RAY DIFFRACTIONTorsion NCS2.46425211933
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS1.81780479019
ens_3d_4IX-RAY DIFFRACTIONTorsion NCS4.28768705718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.210.3212270.26584182X-RAY DIFFRACTION99.98
2.21-2.240.31022230.2684238X-RAY DIFFRACTION99.96
2.24-2.270.33062020.274267X-RAY DIFFRACTION99.98
2.27-2.30.32382330.26784232X-RAY DIFFRACTION99.96
2.3-2.330.3252280.25494248X-RAY DIFFRACTION99.98
2.33-2.360.2852230.24854205X-RAY DIFFRACTION99.98
2.36-2.390.30292370.24834243X-RAY DIFFRACTION100
2.39-2.430.3172370.24764236X-RAY DIFFRACTION99.93
2.43-2.470.29012500.24564216X-RAY DIFFRACTION99.98
2.47-2.510.30522170.2374285X-RAY DIFFRACTION100
2.51-2.550.29162110.23394196X-RAY DIFFRACTION99.95
2.55-2.60.28892470.22594292X-RAY DIFFRACTION100
2.6-2.650.32752060.2254200X-RAY DIFFRACTION100
2.65-2.70.30372180.22794282X-RAY DIFFRACTION99.96
2.7-2.760.27782290.22834228X-RAY DIFFRACTION99.98
2.76-2.820.28412350.22864253X-RAY DIFFRACTION99.98
2.82-2.890.28642210.22294268X-RAY DIFFRACTION99.98
2.89-2.970.2762490.22764148X-RAY DIFFRACTION99.91
2.97-3.060.26872020.2124298X-RAY DIFFRACTION99.98
3.06-3.160.24682380.20474243X-RAY DIFFRACTION100
3.16-3.270.25442450.19774220X-RAY DIFFRACTION100
3.27-3.40.22752470.19624250X-RAY DIFFRACTION99.96
3.4-3.560.2532130.19324243X-RAY DIFFRACTION100
3.56-3.740.23682490.17784236X-RAY DIFFRACTION100
3.74-3.980.20742370.17564269X-RAY DIFFRACTION99.98
3.98-4.280.19712380.15264234X-RAY DIFFRACTION100
4.29-4.720.17462120.14134293X-RAY DIFFRACTION99.98
4.72-5.40.17552160.14454275X-RAY DIFFRACTION99.98
5.4-6.790.19022140.17074289X-RAY DIFFRACTION100
6.79-38.030.18432490.1644302X-RAY DIFFRACTION99.82

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