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- PDB-4jzj: Crystal Structure of Receptor-Fab Complex -

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Basic information

Entry
Database: PDB / ID: 4jzj
TitleCrystal Structure of Receptor-Fab Complex
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • Interleukin-3 receptor subunit alpha
KeywordsCYTOKINE RECEPTOR/IMMUNE SYSTEM / receptor-fab complex / CYTOKINE RECEPTOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


interleukin-3 receptor activity / interleukin-3-mediated signaling pathway / cytokine receptor activity / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cytokine-mediated signaling pathway / RAF/MAP kinase cascade / receptor complex / external side of plasma membrane / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3850 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin-like - #3850 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-3 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsBroughton, S.E. / Parker, M.W.
CitationJournal: Cell Rep / Year: 2014
Title: Dual mechanism of interleukin-3 receptor blockade by an anti-cancer antibody
Authors: Broughton, S.E. / Hercus, T.R. / Hardy, M.P. / McClure, B.J. / Nero, T.L. / Dottore, M. / Huynh, H. / Braley, H. / Barry, E.F. / Kan, W.L. / Dhagat, U. / Scotney, P. / Hartman, D. / ...Authors: Broughton, S.E. / Hercus, T.R. / Hardy, M.P. / McClure, B.J. / Nero, T.L. / Dottore, M. / Huynh, H. / Braley, H. / Barry, E.F. / Kan, W.L. / Dhagat, U. / Scotney, P. / Hartman, D. / Busfield, S.J. / Owczarek, C.M. / Nash, A.D. / Wilson, N.J. / Parker, M.W. / Lopez, A.F.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
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
C: Interleukin-3 receptor subunit alpha
D: Interleukin-3 receptor subunit alpha
A: Fab Heavy Chain
B: Fab Light Chain
H: Fab Heavy Chain
L: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,53013
Polymers162,3086
Non-polymers3,2227
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.300, 120.648, 92.968
Angle α, β, γ (deg.)90.000, 97.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules CD

#1: Protein Interleukin-3 receptor subunit alpha / / IL-3 receptor subunit alpha / IL-3R subunit alpha / IL-3R-alpha / IL-3RA


Mass: 33097.426 Da / Num. of mol.: 2 / Fragment: DOMAIN 2, DOMAIN 3, UNP residues 20-307 / Mutation: Deletion R145, A298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3RA / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26951

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Antibody , 2 types, 4 molecules AHBL

#2: Antibody Fab Heavy Chain / Fragment antigen-binding


Mass: 23799.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The Fab fragment was prepared by papain digestion of MAb and Protein A removal of undigested immunoglobulin and Fc fragment.
Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 24256.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The Fab fragment was prepared by papain digestion of MAb and Protein A removal of undigested immunoglobulin and Fc fragment.
Source: (natural) Mus musculus (house mouse)

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Sugars , 4 types, 5 molecules

#4: 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)-[beta-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1203.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4-2/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 513.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1221m-1b_1-5]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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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Non-polymers , 2 types, 41 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS SEQUENCE IS A RESULT OF POLYMORPHIC VARIATION

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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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 22% PEG 3350, 200mM Sodium Malonate, 100mM Citrate Buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 47603 / Num. obs: 47194 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 50.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 25
Reflection shellResolution: 2.8→2.85 Å / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.75 Å49.59 Å
Translation2.75 Å49.59 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
PHENIXdev_1218refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.801→49.675 Å / Occupancy max: 1 / Occupancy min: 0.96 / FOM work R set: 0.7957 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2379 5.04 %RANDOM
Rwork0.1849 ---
obs0.1878 47185 99.12 %-
all-47191 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.29 Å2 / Biso mean: 50.3063 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: LAST / Resolution: 2.801→49.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10719 0 214 39 10972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111222
X-RAY DIFFRACTIONf_angle_d1.45615220
X-RAY DIFFRACTIONf_chiral_restr0.0871685
X-RAY DIFFRACTIONf_plane_restr0.0061915
X-RAY DIFFRACTIONf_dihedral_angle_d17.064161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8012-2.85840.36771280.29342549267796
2.8584-2.92050.34791460.276726642810100
2.9205-2.98840.32921520.259326222774100
2.9884-3.06320.38841500.251326132763100
3.0632-3.1460.34521570.254826332790100
3.146-3.23850.28491260.24126562782100
3.2385-3.3430.30421380.229226302768100
3.343-3.46250.30541330.214726562789100
3.4625-3.60110.27881540.198826262780100
3.6011-3.76490.25391480.18822626277499
3.7649-3.96330.2491390.180826482787100
3.9633-4.21150.20981480.16772653280199
4.2115-4.53650.19081320.1422620275299
4.5365-4.99270.19081350.13222639277499
4.9927-5.71420.18321300.15022656278699
5.7142-7.19580.25371270.18762677280499
7.1958-49.68260.22191360.18162638277497
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)
12.4690.94411.64161.56691.44462.8911-0.16510.97910.1014-0.06490.0632-0.40890.03140.8011-0.0150.26080.06970.17050.7175-0.00670.59165.524630.6333-32.4702
22.34810.90830.79373.1708-2.93627.2325-0.0053-0.17460.63450.166-0.1589-0.4496-0.08270.8150.18690.28250.0721-0.07310.3287-0.10090.757811.867539.0804-1.5771
32.95310.52880.09131.3977-0.12882.48720.19730.379-0.705-0.18330.1417-0.48210.53790.3438-0.09870.35350.13760.01850.2358-0.14320.5867-5.077512.6118-23.8501
42.40690.50690.13166.1522-0.8952.0814-0.0414-0.72130.58290.58730.0480.7176-0.3466-0.6062-0.06960.35050.2551-0.00750.6834-0.10020.582-3.401936.86954.9507
55.69260.6138-0.70212.77850.21558.63010.1414-0.1179-0.4868-0.0494-0.0607-0.00460.5068-0.1899-0.05770.2427-0.0504-0.00980.22010.01460.286765.30511.5029-9.6055
64.6380.63971.75173.06751.28093.0713-0.3265-0.25740.1987-0.12120.2013-0.1274-0.0778-0.07940.14230.29660.06770.01330.2763-0.05920.19167.041336.3649-27.3895
71.7823-2.24962.62013.5467-3.4474.6687-0.3725-0.40110.5221-0.33860.52111.0869-0.7591-0.68150.01470.8840.1425-0.33750.62050.04440.955143.288849.57-44.6499
84.26081.0993-0.95653.64831.7051.9654-0.11591.163-0.8068-0.5515-0.0152-0.21070.75720.86250.03790.7530.12520.1030.8705-0.20720.4031-9.567616.6503-52.5413
94.27910.20690.8330.9007-0.14128.0451-0.19150.2804-0.1239-0.32820.17780.082-0.0488-0.23390.09260.6672-0.0911-0.10230.2713-0.04950.3129-36.052226.4687-53.9123
105.49051.1943-2.97844.6936-0.22733.79490.0189-0.67450.13450.70240.15410.72490.5211-1.17870.02770.5053-0.02380.04940.90080.06530.4025-44.561624.6844-22.9009
114.19690.889-1.35151.9770.83114.0612-0.1907-0.2147-0.23510.3029-0.2713-0.07910.08070.34950.37620.4208-0.1396-0.06560.24520.12160.27650.485710.615111.799
124.14080.59030.16083.5154-0.21012.46580.2727-1.1669-0.46450.4686-0.2352-0.2751-0.2252-0.042-0.04520.4112-0.1006-0.06280.45070.03030.206319.16166.314327.6707
135.80482.4545-0.1543.51960.58774.259-0.34561.0468-0.6318-0.31860.2251-0.04010.21780.28060.12820.3226-0.04080.01360.5154-0.12840.365539.7511-0.6935-4.42
144.31-1.3595-1.24835.69582.47964.01060.1529-0.07480.04830.0257-0.14590.2874-0.3372-0.5241-0.02930.28340.01410.00420.38290.010.20299.110610.272415.2145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:133)A1 - 133
2X-RAY DIFFRACTION2(CHAIN A AND RESID 141:221)A141 - 221
3X-RAY DIFFRACTION3(CHAIN B AND RESID 1:112)B1 - 112
4X-RAY DIFFRACTION4(CHAIN B AND RESID 113:219)B113 - 219
5X-RAY DIFFRACTION5(CHAIN C AND RESID 25:97)C25 - 97
6X-RAY DIFFRACTION6(CHAIN C AND RESID 98:211)C98 - 211
7X-RAY DIFFRACTION7(CHAIN C AND RESID 212:289)C212 - 289
8X-RAY DIFFRACTION8(CHAIN D AND RESID 25:100)D25 - 100
9X-RAY DIFFRACTION9(CHAIN D AND RESID 101:205)D101 - 205
10X-RAY DIFFRACTION10(CHAIN D AND RESID 206:290)D206 - 290
11X-RAY DIFFRACTION11(CHAIN H AND RESID 1:120)H1 - 120
12X-RAY DIFFRACTION12(CHAIN H AND RESID 121:221)H121 - 221
13X-RAY DIFFRACTION13(CHAIN L AND RESID 1:113)L1 - 113
14X-RAY DIFFRACTION14(CHAIN L AND RESID 114:219)L114 - 219

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