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- PDB-6o4p: The crystal structure of the interleukin 11 alpha receptor -

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Basic information

Entry
Database: PDB / ID: 6o4p
TitleThe crystal structure of the interleukin 11 alpha receptor
ComponentsInterleukin-11 receptor subunit alpha
KeywordsPROTEIN BINDING / cytokine / interleukin / receptor
Function / homology
Function and homology information


interleukin-11 receptor activity / interleukin-11 binding / head development / interleukin-11-mediated signaling pathway / developmental process / IL-6-type cytokine receptor ligand interactions / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / receptor complex / external side of plasma membrane ...interleukin-11 receptor activity / interleukin-11 binding / head development / interleukin-11-mediated signaling pathway / developmental process / IL-6-type cytokine receptor ligand interactions / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / receptor complex / external side of plasma membrane / positive regulation of cell population proliferation / extracellular region / plasma membrane
Similarity search - Function
Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-11 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.429 Å
AuthorsAizel, K. / Metcalfe, R.D. / Griffin, M.D.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The structure of the extracellular domains of human interleukin 11 alpha receptor reveals mechanisms of cytokine engagement.
Authors: Metcalfe, R.D. / Aizel, K. / Zlatic, C.O. / Nguyen, P.M. / Morton, C.J. / Lio, D.S. / Cheng, H.C. / Dobson, R.C.J. / Parker, M.W. / Gooley, P.R. / Putoczki, T.L. / Griffin, M.D.W.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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: Interleukin-11 receptor subunit alpha
B: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,87416
Polymers76,4232
Non-polymers2,45114
Water0
1
A: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7589
Polymers38,2121
Non-polymers1,5468
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1167
Polymers38,2121
Non-polymers9056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.456, 171.456, 107.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Interleukin-11 receptor subunit alpha / / IL-11RA


Mass: 38211.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11RA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q14626
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4

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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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.6 M Ammonium sulfate, 0.02 M NaCl, 67 mM NDSB-195, 0.1 M HEPES pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2017
RadiationMonochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection shellResolution: 3.43→3.7 Å / CC1/2: 0.436 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.429→45.674 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 30.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 612 4.72 %RANDOM
Rwork0.2439 ---
obs0.2464 12962 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.9 Å2
Refinement stepCycle: LAST / Resolution: 3.429→45.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 0 147 0 4580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024735
X-RAY DIFFRACTIONf_angle_d0.5816530
X-RAY DIFFRACTIONf_dihedral_angle_d2.512754
X-RAY DIFFRACTIONf_chiral_restr0.041708
X-RAY DIFFRACTIONf_plane_restr0.004838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4287-3.77360.34841600.31262984X-RAY DIFFRACTION99
3.7736-4.31930.28391580.24833048X-RAY DIFFRACTION100
4.3193-5.44040.2791460.21123069X-RAY DIFFRACTION100
5.4404-45.67810.29381480.23473249X-RAY DIFFRACTION99
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)
12.4231-1.0642-1.94341.7778-0.25293.15060.2076-0.42710.50690.0473-0.36350.8524-0.8142-0.7458-0.02790.3790.1430.01360.5555-0.24590.525-140.87623.8342-18.4649
20.8679-0.428-0.68410.61580.49020.6286-0.274-0.1962-0.15080.20340.1422-0.0430.05950.1215-0.50930.47320.25290.15220.1775-0.2614-0.0092-109.37666.3239-24.9942
31.0785-0.0578-0.29741.02730.322.067-0.01510.1179-0.1995-0.4360.12780.12150.1874-0.17620.43730.36970.0945-0.05830.1893-0.26170.0268-89.397-10.058-49.065
43.1587-1.33581.32490.91180.55994.171-0.546-0.5686-0.1021-0.4608-0.0874-0.67470.2191-0.7463-0.62171.46070.22510.92840.95650.04321.9924-72.3048-18.9264-81.1529
52.44351.07090.81963.78772.55155.7280.0619-0.0762-0.41630.204-0.26120.17060.9353-0.45690.06930.6184-0.05010.0690.654-0.19880.1977-132.2654-4.6517-44.362
64.04971.8551.63284.38532.26051.9913-0.49180.49950.2608-0.76760.1904-0.1554-0.33790.08110.04350.33330.1475-0.01140.3421-0.06350.1691-116.660628.1173-38.0121
74.57050.4080.91735.3076-0.09255.5319-0.2557-0.07060.01470.00070.2512-0.3864-0.3765-0.4351-0.09490.37980.1161-0.06360.18080.05150.2818-108.386148.6334-11.5095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 304 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88 )
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 194 )
7X-RAY DIFFRACTION7chain 'B' and (resid 195 through 296 )

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