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- PDB-6yio: CRYSTAL STRUCTURE OF FAB RG6292 IN COMPLEX WITH CD25 ECD -

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Basic information

Entry
Database: PDB / ID: 6yio
TitleCRYSTAL STRUCTURE OF FAB RG6292 IN COMPLEX WITH CD25 ECD
Components
  • FAB FRAGMENT HEAVY CHAIN
  • FAB FRGAMENT LIGHT CHAIN
  • Interleukin-2 receptor subunit alpha
KeywordsIMMUNE SYSTEM / ANTIBODY / CD25 ECD / FAB RG6292 / IL2Ra
Function / homology
Function and homology information


regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus / Interleukin-2 signaling / activation-induced cell death of T cells / positive regulation of T cell differentiation / positive regulation of activated T cell proliferation / Interleukin receptor SHC signaling / Notch signaling pathway / negative regulation of T cell proliferation / negative regulation of inflammatory response / RAF/MAP kinase cascade / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Interleukin-2 receptor alpha / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBenz, J. / Koll, H. / Leibrock, L.
CitationJournal: Nat Cancer / Year: 2020
Title: CD25-T reg -depleting antibodies preserving IL-2 signaling on effector T cells enhance effector activation and antitumor immunity.
Authors: Solomon, I. / Amann, M. / Goubier, A. / Vargas, F.A. / Zervas, D. / Qing, C. / Henry, J.Y. / Ghorani, E. / Akarca, A.U. / Marafioti, T. / Sledzinska, A. / Sunderland, M.W. / Demane, D.F. / ...Authors: Solomon, I. / Amann, M. / Goubier, A. / Vargas, F.A. / Zervas, D. / Qing, C. / Henry, J.Y. / Ghorani, E. / Akarca, A.U. / Marafioti, T. / Sledzinska, A. / Sunderland, M.W. / Demane, D.F. / Clancy, J.R. / Georgiou, A. / Salimu, J. / Merchiers, P. / Brown, M.A. / Flury, R. / Eckmann, J. / Murgia, C. / Sam, J. / Jacobsen, B. / Marrer-Berger, E. / Boetsch, C. / Belli, S. / Leibrock, L. / Benz, J. / Koll, H. / Sutmuller, R. / Peggs, K.S. / Quezada, S.A.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Interleukin-2 receptor subunit alpha
H: FAB FRAGMENT HEAVY CHAIN
L: FAB FRGAMENT LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)70,2643
Polymers70,2643
Non-polymers00
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-27 kcal/mol
Surface area26980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.381, 44.321, 140.085
Angle α, β, γ (deg.)90.000, 92.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-2 receptor subunit alpha / IL2-RA / TAC antigen / p55


Mass: 23219.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01589
#2: Antibody FAB FRAGMENT HEAVY CHAIN


Mass: 23646.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody FAB FRGAMENT LIGHT CHAIN


Mass: 23397.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% v/v PEG Smear Medium (12.5% w/v PEG 3350, 12.5% w/v PEG 4000, 12.5% w/v PEG 2000, 12.5% w/v PEG 5000 MME) 0.1M SODIUM ACETATE, PH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99982 Å / Relative weight: 1
ReflectionResolution: 1.83→69.98 Å / Num. obs: 56064 / % possible obs: 99.9 % / Redundancy: 3.39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.7
Reflection shellResolution: 1.83→1.92 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 7407 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5I

2b5i


Resolution: 1.83→69.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 2888 5.15 %RANDOM
Rwork0.2025 ---
obs0.2039 56041 99.9 %-
Displacement parametersBiso max: 95.02 Å2 / Biso mean: 33.89 Å2 / Biso min: 16.95 Å2
Baniso -1Baniso -2Baniso -3
1-4.6253 Å20 Å22.1963 Å2
2---6.3522 Å20 Å2
3---1.727 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.83→69.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 0 589 4878
Biso mean---42.25 -
Num. residues----563
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1496SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes748HARMONIC5
X-RAY DIFFRACTIONt_it4451HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion592SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3945SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4451HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6060HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion15.98
LS refinement shellResolution: 1.83→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3161 60 5.35 %
Rwork0.2736 1061 -
all0.2757 1121 -
obs--99.74 %
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)
12.8223-1.85110.34683.1519-0.08191.48030.03660.03180.01210.0311-0.07970.2003-0.0355-0.16280.043-0.056-0.0158-0.0304-0.08940.0137-0.1547-26.666812.03748.4757
21.3568-0.03491.00850.32110.13561.2669-0.0575-0.07090.0466-0.07780.0221-0.0326-0.0923-0.0060.0354-0.06320.00290.0108-0.07640.0002-0.0539-0.80390.68441.8246
30.7396-0.02780.71340.1829-0.12561.13190.08740.026-0.1618-0.04180.02080.0220.15910.138-0.1082-0.06480.0252-0.0009-0.0688-0.025-0.03848.464-14.910940.3837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 164
2X-RAY DIFFRACTION2{ H|* }H1 - 223
3X-RAY DIFFRACTION3{ L|* }L1 - 213

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