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- PDB-5eh1: Crystal structure of the extracellular part of receptor 2 of huma... -

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Basic information

Entry
Database: PDB / ID: 5eh1
TitleCrystal structure of the extracellular part of receptor 2 of human interferon gamma
ComponentsInterferon gamma receptor 2
KeywordsCYTOKINE / interferon gamma / immunity / fibronectin III domain
Function / homology
Function and homology information


type II interferon receptor activity / type III interferon-mediated signaling pathway / cytokine receptor activity / IFNG signaling activates MAPKs / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / microglial cell activation / response to virus / cytoplasmic vesicle membrane / cellular response to virus ...type II interferon receptor activity / type III interferon-mediated signaling pathway / cytokine receptor activity / IFNG signaling activates MAPKs / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / microglial cell activation / response to virus / cytoplasmic vesicle membrane / cellular response to virus / cytokine-mediated signaling pathway / Interferon gamma signaling / defense response to virus / Potential therapeutics for SARS / cell surface receptor signaling pathway / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / 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
CYSTEINE / Interferon gamma receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKolenko, P. / Mikulecky, P. / Zahradnik, J. / Dohnalek, J. / Koval, T. / Cerny, J. / Necasova, I. / Schneider, B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity.
Authors: Mikulecky, P. / Zahradnik, J. / Kolenko, P. / Cerny, J. / Charnavets, T. / Kolarova, L. / Necasova, I. / Pham, P.N. / Schneider, B.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon gamma receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2708
Polymers26,2081
Non-polymers1,0617
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint10 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.102, 58.102, 377.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein Interferon gamma receptor 2 / / IFN-gamma-R2 / Interferon gamma receptor accessory factor 1 / AF-1 / Interferon gamma transducer 1


Mass: 26208.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR2, IFNGT1 / Plasmid: pMT-BiP-V5-His_A
Details (production host): pMT-BiP-V5-His_A vector co-transfected with the pCoBlast for selection
Cell line (production host): Schneider 2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P38484
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 5.0 + 10% PEG 6000, cryoprotected in 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.8→62.88 Å / Num. obs: 36722 / % possible obs: 99.9 % / Redundancy: 18.8 % / Biso Wilson estimate: 20 Å2 / Net I/σ(I): 17.6
Reflection shellResolution: 1.799→1.91 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2455 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MxCuBEdata collection
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→62.88 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 2.254 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1820 5 %Random selection
Rwork0.19 ---
obs0.191 36722 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→62.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 67 311 2049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021876
X-RAY DIFFRACTIONr_bond_other_d0.0020.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.962575
X-RAY DIFFRACTIONr_angle_other_deg0.90134001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9945229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42823.64785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.815290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3521510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.872.39864
X-RAY DIFFRACTIONr_mcbond_other1.8622.385863
X-RAY DIFFRACTIONr_mcangle_it3.0053.5561080
X-RAY DIFFRACTIONr_mcangle_other3.0063.5611081
X-RAY DIFFRACTIONr_scbond_it2.4492.7121012
X-RAY DIFFRACTIONr_scbond_other2.4472.7121012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9543.9531482
X-RAY DIFFRACTIONr_long_range_B_refined7.55221.6322251
X-RAY DIFFRACTIONr_long_range_B_other6.56620.1192084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 144 -
Rwork0.288 2455 -
obs--99.39 %

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