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- PDB-7opb: IL7R in complex with an antagonist -

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Basic information

Entry
Database: PDB / ID: 7opb
TitleIL7R in complex with an antagonist
Components
  • IL7R binder
  • Interleukin-7 receptor subunit alpha
KeywordsPROTEIN BINDING / protein binder / IL7R / antagonist
Function / homology
Function and homology information


interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis ...interleukin-7 receptor activity / positive regulation of receptor signaling pathway via STAT / negative regulation of T cell mediated cytotoxicity / regulation of DNA recombination / positive regulation of T cell differentiation in thymus / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis / B cell homeostasis / hemopoiesis / lymph node development / Interleukin-7 signaling / antigen binding / positive regulation of receptor signaling pathway via JAK-STAT / clathrin-coated endocytic vesicle membrane / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / gene expression / T cell differentiation in thymus / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Interleukin-7 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 Å
AuthorsMarkovic, I. / Verschueren, K.H.G. / Verstraete, K. / Savvides, S.N.
CitationJournal: Nature / Year: 2022
Title: Design of protein-binding proteins from the target structure alone.
Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. ...Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. / Phal, A. / Yang, A. / Kozodoy, L. / DeWitt, M. / Picton, L. / Miller, L. / Strauch, E.M. / DeBouver, N.D. / Pires, A. / Bera, A.K. / Halabiya, S. / Hammerson, B. / Yang, W. / Bernard, S. / Stewart, L. / Wilson, I.A. / Ruohola-Baker, H. / Schlessinger, J. / Lee, S. / Savvides, S.N. / Garcia, K.C. / Baker, D.
History
DepositionMay 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-7 receptor subunit alpha
B: Interleukin-7 receptor subunit alpha
C: Interleukin-7 receptor subunit alpha
D: IL7R binder
E: IL7R binder
F: IL7R binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46612
Polymers87,9176
Non-polymers5496
Water5,567309
1
A: Interleukin-7 receptor subunit alpha
D: IL7R binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5184
Polymers29,3062
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-1 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: Interleukin-7 receptor subunit alpha
E: IL7R binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4744
Polymers29,3062
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-4 kcal/mol
Surface area13820 Å2
MethodPISA
3
C: Interleukin-7 receptor subunit alpha
F: IL7R binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4744
Polymers29,3062
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-5 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.182, 132.182, 58.877
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein Interleukin-7 receptor subunit alpha / IL-7 receptor subunit alpha / IL-7R subunit alpha / IL-7R-alpha / IL-7RA / CDw127


Mass: 22862.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL7R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16871
#2: Protein IL7R binder


Mass: 6443.422 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 315 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0,1 M Phosphate/Citrate, 25% v/v PEG Smear Low Cryoprotected with 25% PEG-400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.144→43.96 Å / Num. obs: 62839 / % possible obs: 99.6 % / Redundancy: 8.19 % / Biso Wilson estimate: 34.17 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.08 / Rrim(I) all: 0.204 / Χ2: 1.02 / Net I/av σ(I): 6.92 / Net I/σ(I): 6.92
Reflection shellResolution: 2.144→2.27 Å / Mean I/σ(I) obs: 1.04 / Num. unique obs: 9978 / CC1/2: 0.442 / Rpim(I) all: 0.868 / Rrim(I) all: 1.94 / Χ2: 0.98 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DI2

3di2


Resolution: 2.144→43.96 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 3093 -RANDOM
Rwork0.1938 ---
obs0.1946 62832 99.6 %-
Displacement parametersBiso mean: 58.66 Å2
Baniso -1Baniso -2Baniso -3
1--4.6303 Å20 Å20 Å2
2---4.6303 Å20 Å2
3---9.2606 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.144→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 0 36 309 6514
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086367HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.978575HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2319SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1054HARMONIC5
X-RAY DIFFRACTIONt_it6337HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion806SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4639SEMIHARMONIC0
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion16.61
LS refinement shellResolution: 2.144→2.16 Å
RfactorNum. reflection% reflection
Rfree0.2104 62 -
Rwork0.2032 --
obs--83.61 %

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