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- PDB-4yqx: Mouse IL-2 Bound to JES6-1 scFv Fragment -

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Basic information

Entry
Database: PDB / ID: 4yqx
TitleMouse IL-2 Bound to JES6-1 scFv Fragment
Components
  • Interleukin-2
  • JES6-1 VH domain
  • JES6-1 VL domain
KeywordsCYTOKINE/IMMUNE SYSTEM / chemokine / antibody / complex / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / protein kinase C-activating G protein-coupled receptor signaling pathway / tyrosine phosphorylation of STAT protein / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / gene expression / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle ...Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.826 Å
AuthorsSpangler, J.B. / Luca, V.C. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI108626 United States
CitationJournal: Immunity / Year: 2015
Title: Antibodies to Interleukin-2 Elicit Selective T Cell Subset Potentiation through Distinct Conformational Mechanisms.
Authors: Spangler, J.B. / Tomala, J. / Luca, V.C. / Jude, K.M. / Dong, S. / Ring, A.M. / Votavova, P. / Pepper, M. / Kovar, M. / Garcia, K.C.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Source and taxonomy
Revision 1.2Jul 26, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 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.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _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
Revision 2.1Sep 27, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: JES6-1 VH domain
L: JES6-1 VL domain
A: Interleukin-2
N: JES6-1 VH domain
O: JES6-1 VL domain
M: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9548
Polymers82,8136
Non-polymers1,1412
Water1,45981
1
H: JES6-1 VH domain
L: JES6-1 VL domain
A: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1234
Polymers41,4063
Non-polymers7171
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: JES6-1 VH domain
O: JES6-1 VL domain
M: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8314
Polymers41,4063
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.024, 99.024, 198.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain M
12chain H
22chain N
13chain L
23chain O

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERchain AAC26 - 1474 - 125
21GLYGLYSERSERchain MMF25 - 1473 - 125
12GLUGLUSERSERchain HHA4 - 1243 - 123
22GLUGLUSERSERchain NND4 - 1243 - 123
13GLYGLYALAALAchain LLB2 - 1181 - 117
23GLYGLYLYSLYSchain OOE2 - 1161 - 115

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules HNLO

#1: Antibody JES6-1 VH domain


Mass: 13802.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody JES6-1 VL domain


Mass: 12648.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Trichoplusia ni (cabbage looper)

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Protein / Non-polymers , 2 types, 83 molecules AM

#3: Protein Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 14956.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il2, Il-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04351
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.4
Details: 0.1 M Bis-Tris propane, pH 6.4, 0.2 M sodium citrate, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.976962 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976962 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 27586 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 53.05 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 0.774 / Net I/av σ(I): 17.474 / Net I/σ(I): 7.7 / Num. measured all: 268758
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.82-2.927.40.67926800.8420.2570.7280.55799.3
2.92-3.049.60.46727010.9410.1550.4930.605100
3.04-3.189.90.33927340.9680.1110.3570.662100
3.18-3.3410.10.25927100.9820.0850.2730.757100
3.34-3.55100.19827240.9860.0650.2090.796100
3.55-3.8310.10.15427410.9920.0510.1620.739100
3.83-4.2110.10.10727450.9960.0350.1120.593100
4.21-4.8210.20.07327840.9970.0240.0771.019100
4.82-6.0710.30.07328100.9970.0240.0770.958100
6.07-509.60.0529570.9990.0170.0530.954100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1951)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B5I

2b5i


Resolution: 2.826→49.512 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 1359 4.94 %
Rwork0.1695 26174 -
obs0.1712 27533 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.72 Å2 / Biso mean: 63.5757 Å2 / Biso min: 20.17 Å2
Refinement stepCycle: final / Resolution: 2.826→49.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 76 81 5825
Biso mean--106.76 49.02 -
Num. residues----719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055880
X-RAY DIFFRACTIONf_angle_d0.8577990
X-RAY DIFFRACTIONf_chiral_restr0.038904
X-RAY DIFFRACTIONf_plane_restr0.0041014
X-RAY DIFFRACTIONf_dihedral_angle_d13.5912169
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1198X-RAY DIFFRACTION6.233TORSIONAL
12M1198X-RAY DIFFRACTION6.233TORSIONAL
21H1120X-RAY DIFFRACTION6.233TORSIONAL
22N1120X-RAY DIFFRACTION6.233TORSIONAL
31L1065X-RAY DIFFRACTION6.233TORSIONAL
32O1065X-RAY DIFFRACTION6.233TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8256-2.92660.32031280.23052382251092
2.9266-3.04370.24331320.195525852717100
3.0437-3.18220.27241360.187226032739100
3.1822-3.350.24091350.183125932728100
3.35-3.55980.20391390.174925992738100
3.5598-3.83460.2171370.173926352772100
3.8346-4.22030.17641400.149926152755100
4.2203-4.83050.16231360.130826572793100
4.8305-6.08420.18251390.160826872826100
6.0842-49.51960.20141370.187828182955100
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)
14.0137-0.1358-0.4835.0107-2.964.712-0.272-0.7937-0.36850.02430.1371-0.08360.06420.16280.07970.2459-0.0311-0.03890.76690.00110.416735.695714.220833.0659
21.49470.1930.19551.612-1.7684.0283-0.0065-1.219-0.15370.7553-0.1654-0.1487-0.0813-0.03750.01090.5054-0.0795-0.02980.97360.20250.67640.71629.577642.4078
35.67664.6097-5.31398.6823-3.63956.745-0.75790.0587-1.1454-0.55920.60840.1380.8506-0.21850.45680.3694-0.0588-0.04880.69470.13460.565536.22772.503434.0713
41.818-0.1231-1.60276.52540.83778.5516-0.1554-1.2530.06011.256-0.4824-1.15910.76220.160.21670.5384-0.3292-0.21031.1514-0.07650.421913.865927.048762.1439
55.33140.29110.43954.68980.54954.70780.0579-0.97280.58630.4558-0.2164-0.1881-0.13080.02110.10320.3617-0.1448-0.07840.4998-0.05940.36710.289632.9452.8813
62.2260.27770.4074.277-2.38728.43880.3667-0.53580.12260.3969-0.0570.01310.10190.2584-0.29190.2995-0.1935-0.03520.5155-0.03130.34427.531626.857654.4208
73.6232-0.33280.0972.10260.12811.6672-0.32410.1598-0.3134-0.2880.5992-0.49580.1811-0.2136-0.23560.3099-0.1047-0.00190.4056-0.02410.3587-8.892314.413145.5601
83.25850.63650.47066.3203-1.21871.6719-0.0265-0.0086-0.1159-0.05070.0634-0.32020.01750.0705-0.05660.2015-0.0970.00870.3612-0.02130.3145-0.887318.030841.5942
94.6316-1.58830.55944.5904-0.06421.8337-0.07090.02160.5496-0.4046-0.17920.4817-0.3109-0.01440.27010.4434-0.1581-0.05990.427-0.00460.7021-2.26744.292136.4613
104.8009-0.76990.6412.1382-1.11071.4043-0.49860.56810.65-0.55230.33850.4203-0.0812-0.23150.07880.6884-0.1703-0.20980.49220.04890.7749-6.471251.796929.7954
119.36454.5722-0.85893.84860.57386.9344-0.5337-0.39981.3333-0.0921-0.13851.9213-0.2424-0.62520.49870.4474-0.0636-0.11520.38730.04470.7872-10.57547.0640.7844
124.6137-0.33161.26863.90.32947.74490.3460.30990.65-0.7607-0.3805-0.1563-0.0940.3053-0.1850.2797-0.00960.09560.38250.04210.413729.564217.4663-0.3749
132.49071.35741.046.515-0.28285.49390.03430.01460.0212-0.0965-0.0702-0.2440.09730.47820.01360.1783-0.00430.03330.4237-0.01280.259232.999918.230210.7996
144.8446-0.63831.87574.12142.25828.15610.1205-0.00770.1179-0.3353-0.1475-0.0701-0.25730.0224-0.04040.1133-0.07720.07450.23850.04940.230126.308617.8039.3862
157.456-6.03135.44619.0175-4.22394.40710.0057-0.11090.61790.13-0.1576-0.49110.0903-0.04660.02610.2466-0.05980.06180.45730.05530.30777.53315.462221.0044
165.1921-1.4076-1.29174.1878-2.31875.1322-0.046-0.19620.48080.186-0.0425-0.3057-0.258-0.18650.0510.2081-0.11780.02520.3032-0.02090.255918.158223.929122.832
178.2333-2.5893.5072.0605-0.98144.83580.0038-0.37380.53660.2262-0.0475-0.3242-0.3206-0.0373-0.05530.2257-0.10960.05430.40960.00440.284911.302422.279221.7048
187.6983-3.66221.48966.7757-2.55073.42490.1695-0.2871-0.6869-0.21010.07360.28230.3685-0.1329-0.27840.2161-0.04850.07330.29290.00330.15939.608416.763814.7172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 26:58)A26 - 58
2X-RAY DIFFRACTION2(chain A and resid 59:121)A59 - 121
3X-RAY DIFFRACTION3(chain A and resid 122:147)A122 - 147
4X-RAY DIFFRACTION4(chain N and resid 4:23)N4 - 23
5X-RAY DIFFRACTION5(chain N and resid 24:87)N24 - 87
6X-RAY DIFFRACTION6(chain N and resid 88:124)N88 - 124
7X-RAY DIFFRACTION7(chain O and resid 3:27)O3 - 27
8X-RAY DIFFRACTION8(chain O and resid 28:116)O28 - 116
9X-RAY DIFFRACTION9(chain M and resid 26:62)M26 - 62
10X-RAY DIFFRACTION10(chain M and resid 63:124)M63 - 124
11X-RAY DIFFRACTION11(chain M and resid 125:147)M125 - 147
12X-RAY DIFFRACTION12(chain H and resid 4:22)H4 - 22
13X-RAY DIFFRACTION13(chain H and resid 23:87)H23 - 87
14X-RAY DIFFRACTION14(chain H and resid 88:124)H88 - 124
15X-RAY DIFFRACTION15(chain L and resid 3:28)L3 - 28
16X-RAY DIFFRACTION16(chain L and resid 29:68)L29 - 68
17X-RAY DIFFRACTION17(chain L and resid 69:103)L69 - 103
18X-RAY DIFFRACTION18(chain L and resid 104:117)L104 - 117

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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