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- PDB-5dwu: Beta common receptor in complex with a Fab -

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Basic information

Entry
Database: PDB / ID: 5dwu
TitleBeta common receptor in complex with a Fab
Components
  • (Cytokine receptor common subunit beta) x 2
  • Fab - Heavy Chain
  • Fab - Light Chain
KeywordsIMMUNE SYSTEM / Fab complex / antigen recognition / therapeutic antibody
Function / homology
Function and homology information


Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 ...Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / cytokine receptor activity / cell surface receptor signaling pathway via JAK-STAT / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / cytokine-mediated signaling pathway / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...: / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Interferon-alpha/beta receptor, fibronectin type III / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.97 Å
AuthorsDhagat, U. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Mabs / Year: 2016
Title: CSL311, a novel, potent, therapeutic monoclonal antibody for the treatment of diseases mediated by the common beta chain of the IL-3, GM-CSF and IL-5 receptors.
Authors: Panousis, C. / Dhagat, U. / Edwards, K.M. / Rayzman, V. / Hardy, M.P. / Braley, H. / Gauvreau, G.M. / Hercus, T.R. / Smith, S. / Sehmi, R. / McMillan, L. / Dottore, M. / McClure, B.J. / ...Authors: Panousis, C. / Dhagat, U. / Edwards, K.M. / Rayzman, V. / Hardy, M.P. / Braley, H. / Gauvreau, G.M. / Hercus, T.R. / Smith, S. / Sehmi, R. / McMillan, L. / Dottore, M. / McClure, B.J. / Fabri, L.J. / Vairo, G. / Lopez, A.F. / Parker, M.W. / Nash, A.D. / Wilson, N.J. / Wilson, M.J. / Owczarek, C.M.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytokine receptor common subunit beta
B: Cytokine receptor common subunit beta
H: Fab - Heavy Chain
L: Fab - Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6096
Polymers96,1674
Non-polymers4422
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-41 kcal/mol
Surface area41150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.953, 71.289, 221.234
Angle α, β, γ (deg.)90.000, 102.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 25457.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927
#2: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 23318.045 Da / Num. of mol.: 1 / Mutation: N106Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927
#3: Antibody Fab - Heavy Chain


Mass: 24132.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab - Light Chain


Mass: 23258.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris 8, 25% - 35% PEG200

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.97→49.98 Å / Num. obs: 13201 / % possible obs: 98.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 143.95 Å2 / CC1/2: 0.932 / Rmerge(I) obs: 0.904 / Rpim(I) all: 0.331 / Net I/σ(I): 3.3 / Num. measured all: 97186 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.97-4.434.30.9261.41541735450.7350.47793.4
8.87-49.9880.2386.61000512460.9130.0999.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.4data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.97→49.976 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3299 680 5.15 %Random
Rwork0.2885 12514 --
obs0.2905 13194 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 306.58 Å2 / Biso mean: 142.2637 Å2 / Biso min: 28.18 Å2
Refinement stepCycle: final / Resolution: 3.97→49.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 56 0 5232
Biso mean--168.56 --
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035330
X-RAY DIFFRACTIONf_angle_d0.7147312
X-RAY DIFFRACTIONf_chiral_restr0.029858
X-RAY DIFFRACTIONf_plane_restr0.004953
X-RAY DIFFRACTIONf_dihedral_angle_d11.6121685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9664-4.27250.3991570.39652248240591
4.2725-4.70210.29971220.314625712693100
4.7021-5.38180.36771410.288225032644100
5.3818-6.77790.35751350.308525632698100
6.7779-49.97950.2861250.246626292754100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6088-2.0233-0.58234.27773.14345.0990.3025-0.1845-0.1203-0.0527-0.9080.5806-0.2831-0.76140.13331.5982-0.40630.12922.0680.02731.763822.29325.15262.3574
25.4145-2.389-7.05550.83923.17679.14131.751-2.26461.1499-5.2023-1.0785-1.59832.20963.76612.21022.6644-1.0585-0.49792.49840.7471.212142.216424.8293100.2419
33.5097-3.54350.23874.52741.22421.4714-1.80930.96820.3743-0.3818-0.34132.98490.2557-0.08060.26821.4889-0.20480.76072.4943-0.80121.342839.223324.2261107.9888
41.34190.2681-0.24541.64931.30350.9810.535-2.0358-1.0253-0.2386-1.35011.60442.7736-0.73710.05392.2326-0.16060.0442.41270.27551.736532.936725.0897113.1181
54.3357-3.8352-3.80938.70176.53395.3526-3.67490.145-0.28394.5173-1.9740.18281.2641-0.8299-3.28772.67550.7525-0.5943.301-0.01071.101640.369623.514122.9734
61.5046-0.514-2.38452.06722.19211.98790.0918-2.8259-1.52240.6926-1.1871.9344-1.4848-5.2995-1.45841.889-1.11880.31861.73310.64531.503935.633126.1889103.7608
74.0181-1.40191.29733.58630.83862.1425-0.8078-0.8692-1.76760.52210.3699-0.9607-3.275-0.9729-0.13563.7148-0.2650.35091.916-0.34591.456126.237722.06884.3177
81.4129-0.4597-0.46292.46132.4721.0577-0.251-0.0382-0.54391.46870.31750.6820.42720.69050.11612.22620.11110.21552.1531-0.00082.00225.712914.207280.5121
91.45810.3720.35071.06440.38630.82391.4703-0.0810.6963-1.29082.78810.2573-1.9552.85790.08962.4295-0.27140.56422.6137-0.54171.855832.599328.274473.4384
100.73861.10080.07640.45360.65531.2938-0.59371.4852-1.85470.20180.6166-1.8950.22360.3590.07442.2183-0.70570.28122.5029-0.09521.594331.805514.94281.7401
111.79820.7665-0.03281.13781.12961.30130.0747-1.37151.1629-0.93940.5721-0.074-1.1191.24730.06862.0947-0.83340.03273.310.11.712332.978630.03577.9817
122.51440.08730.85756.78424.35435.18690.0259-0.271-0.994-0.3205-0.359-0.55340.42090.4066-0.01671.0781-0.2081-0.01641.35090.14721.511627.246-22.288846.7424
132.4996-2.4574-2.58499.1688-0.78293.815-0.4145-0.8936-0.2509-1.41290.06210.5540.219-0.3543-0.00021.4797-0.16670.03651.50440.02071.276238.782115.485134.8898
142.9522-2.0063-1.14124.0591-1.56422.3345-2.0827-1.6361-3.6657-1.22141.5929-2.1119-2.4677-2.3063-0.0891.41950.25670.1242.30110.21182.066634.917519.426838.6263
153.86830.4825-2.10943.3279-0.57083.19630.5246-0.01550.9216-0.3666-0.0877-0.0594-1.3475-0.4598-0.1381.63730.1162-0.03161.4109-0.12831.189251.298920.019722.5422
161.3272-0.35523.24930.0369-0.61647.43161.06781.1841-2.5051-8.58041.65510.0712-2.283-3.33691.17444.3315-0.7334-0.07972.6386-0.68341.311462.267314.0856-0.7218
172.3438-0.9981-1.66621.9182-0.69242.0152-0.36833.93820.34752.29541.7233.5598-3.5238-0.87150.00072.3861-0.07760.36112.27870.02772.560648.694625.64411.0173
187.7667-0.08340.69955.2919-0.60442.91150.18160.3463-0.17880.17860.0728-0.85250.5592-0.7452-0.17131.1117-0.3073-0.07831.0533-0.04721.285654.24430.261737.4859
191.3359-0.6856-2.0380.06870.50191.9685-0.8921.4631-0.801-0.91010.5953-0.3863-0.80180.0797-0.28052.0519-0.54350.63711.7564-0.03952.163571.195410.832614.0117
201.6987-1.55180.50091.412-0.87441.9609-0.57810.72250.9114-0.9675-0.1773-2.0098-3.231-0.2052-2.28583.2626-1.53210.90432.12010.17242.61366.402534.76976.6451
211.10041.4198-3.08830.7289-2.06313.38610.4449-0.3847-0.1428-0.49930.0544-2.5225-1.17851.4982-0.30431.5349-0.31810.0391.93040.05671.741973.060416.460817.1806
225.2239-1.84771.32224.16631.2021.3307-0.8229-0.52342.4666-3.2927-0.2641-3.62030.13582.1149-0.50732.3869-0.27750.66982.69870.27462.392574.006728.793611.2305
230.76873.1506-1.33051.9138-3.03771.21431.61770.70224.7479-0.01040.8913-4.838-1.0734-0.3309-0.13452.0081-0.29990.75051.77470.18632.711281.574918.255810.7792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 130 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 151 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 180 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 192 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 206 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 230 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 241 through 256 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 257 through 274 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 275 through 286 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 309 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 310 through 324 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 325 through 436 )B0
13X-RAY DIFFRACTION13chain 'H' and (resid 2 through 61 )H0
14X-RAY DIFFRACTION14chain 'H' and (resid 62 through 79 )H0
15X-RAY DIFFRACTION15chain 'H' and (resid 80 through 182 )H0
16X-RAY DIFFRACTION16chain 'H' and (resid 183 through 199 )H0
17X-RAY DIFFRACTION17chain 'H' and (resid 200 through 210 )H0
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 102 )L0
19X-RAY DIFFRACTION19chain 'L' and (resid 103 through 121 )L0
20X-RAY DIFFRACTION20chain 'L' and (resid 122 through 132 )L0
21X-RAY DIFFRACTION21chain 'L' and (resid 133 through 172 )L0
22X-RAY DIFFRACTION22chain 'L' and (resid 173 through 191 )L0
23X-RAY DIFFRACTION23chain 'L' and (resid 192 through 211 )L0

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