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- PDB-6dg5: Structure of a de novo designed Interleukin-2/Interleukin-15 mime... -

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Basic information

Entry
Database: PDB / ID: 6dg5
TitleStructure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg
Components
  • Cytokine receptor common subunit gamma
  • Interleukin-2 receptor subunit betaIL-2 receptor
  • Neoleukin-2/15
KeywordsBIOSYNTHETIC PROTEIN/Protein Binding / cytokine mimetic / cytokine receptor complex / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-Protein Binding complex
Function / homology
Function and homology information


Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / mature B cell differentiation / interleukin-2 receptor activity / Interleukin-15 signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding ...Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / mature B cell differentiation / interleukin-2 receptor activity / Interleukin-15 signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / Interleukin-7 signaling / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / interleukin-9-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / natural killer cell activation / interleukin-15-mediated signaling pathway / cytokine receptor activity / positive regulation of B cell differentiation / cytokine binding / coreceptor activity / positive regulation of phagocytosis / B cell differentiation / cytokine-mediated signaling pathway / T cell differentiation in thymus / gene expression / regulation of gene expression / membrane => GO:0016020 / receptor complex / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / nucleoplasm / plasma membrane
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Fibronectin type III domain ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Fibronectin type III domain / 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
Interleukin-2 receptor subunit beta / Cytokine receptor common subunit gamma
Similarity search - Component
Biological speciessynthetic construct (others)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.516 Å
AuthorsJude, K.M. / Silva, D.-A. / Yu, S. / Baker, D. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
CitationJournal: Nature / Year: 2019
Title: De novo design of potent and selective mimics of IL-2 and IL-15.
Authors: Silva, D.A. / Yu, S. / Ulge, U.Y. / Spangler, J.B. / Jude, K.M. / Labao-Almeida, C. / Ali, L.R. / Quijano-Rubio, A. / Ruterbusch, M. / Leung, I. / Biary, T. / Crowley, S.J. / Marcos, E. / ...Authors: Silva, D.A. / Yu, S. / Ulge, U.Y. / Spangler, J.B. / Jude, K.M. / Labao-Almeida, C. / Ali, L.R. / Quijano-Rubio, A. / Ruterbusch, M. / Leung, I. / Biary, T. / Crowley, S.J. / Marcos, E. / Walkey, C.D. / Weitzner, B.D. / Pardo-Avila, F. / Castellanos, J. / Carter, L. / Stewart, L. / Riddell, S.R. / Pepper, M. / Bernardes, G.J.L. / Dougan, M. / Garcia, K.C. / Baker, D.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neoleukin-2/15
B: Interleukin-2 receptor subunit beta
C: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4687
Polymers60,3823
Non-polymers2,0864
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint29 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.125, 67.914, 172.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Neoleukin-2/15


Mass: 12112.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Interleukin-2 receptor subunit beta / IL-2 receptor / IL-2RB / High affinity IL-2 receptor subunit beta / p70-75


Mass: 24469.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fully glycosylated / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il2rb / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16297
#3: Protein Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2RG / gammaC / p64


Mass: 23799.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il2rg / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P34902

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Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 1219.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-3-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{}}}}[(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 / 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 , 1 types, 13 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.091 M Tris pH 7.5 8 mM imidazole pH 8.0 4.2% DEXTRAN SULFATE 50 mM sodium citrate 2.2 M ammonium sulfate
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.516→47.005 Å / Num. obs: 17512 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 38.2 Å2
Data reduction details: data were subjected to an ellipsoidal resolution cutoff using STARANISO due to severe anisotropy of the data, resulting in low spherical completeness in the outer shells
CC1/2: 0.983 / Rmerge(I) obs: 0.461 / Rpim(I) all: 0.158 / Rrim(I) all: 0.488 / Net I/σ(I): 5.6 / Num. measured all: 163261
Reflection shellResolution: 2.516→2.828 Å / Redundancy: 11.22 % / Rmerge(I) obs: 2.516 / Num. unique obs: 698 / CC1/2: 0.445 / Rpim(I) all: 0.78 / Rrim(I) all: 5.756 / % possible all: 9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS20171111data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.13-2998refinement
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b5i

2b5i


Resolution: 2.516→47.005 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.08
Details: 80% of the observed reflections are used in refinement due to ellipsoidal truncation of the data due to anisotropy
RfactorNum. reflection% reflection
Rfree0.2659 1366 9.81 %
Rwork0.2211 --
obs0.2256 13924 52.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.13 Å2 / Biso mean: 47.0455 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 2.516→47.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 138 13 4100
Biso mean--67.79 27.31 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5163-2.60620.4395140.32561221365
2.6062-2.71060.3671220.36042052279
2.7106-2.83390.3515300.305831934913
2.8339-2.98330.3962440.294348853221
2.9833-3.17020.3295740.272174281631
3.1702-3.41490.33341200.24681209132950
3.4149-3.75840.27372370.2372074231187
3.7584-4.30190.24742760.202223942670100
4.3019-5.41870.23462730.186224392712100
5.4187-47.01360.26152760.232225662842100
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)
12.4853-0.7804-1.88566.05861.15794.28990.14640.12760.1212-0.4116-0.3782-0.1578-0.46480.33880.16060.5436-0.1058-0.06010.1250.07740.240916.4991-14.0395-63.681
21.30090.5338-0.79371.5394-1.93453.5198-0.11330.4106-0.2417-0.1519-0.10460.0727-0.03470.08460.03930.2001-0.01740.00560.2279-0.05570.182519.2978-43.2608-70.543
31.2384-0.6628-0.40996.03741.62880.8549-0.1898-0.2148-0.0440.5351-0.01970.89490.15630.1192-0.03850.2999-0.04660.19330.10110.05760.46594.3521-20.8586-42.5868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' )A0
2X-RAY DIFFRACTION2(chain 'B' )B0
3X-RAY DIFFRACTION3(chain 'C' )C0

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