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- PDB-3s98: human IFNAR1 -

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Basic information

Entry
Database: PDB / ID: 3s98
Titlehuman IFNAR1
ComponentsInterferon alpha/beta receptor 1Interferon-alpha/beta receptor
KeywordsSIGNALING PROTEIN RECEPTOR / human / type I interferons / receptor chain / IFNAR1 / fibronectin type III / type I interferon receptor chain / extracellular space
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta ...type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / response to virus / cellular response to virus / Interferon alpha/beta signaling / late endosome / Potential therapeutics for SARS / response to lipopolysaccharide / lysosome / SARS-CoV-2 activates/modulates innate and adaptive immune responses / plasma membrane
Similarity search - Function
Interferon alpha/beta receptor 1 / 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 ...Interferon alpha/beta receptor 1 / 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
Interferon alpha/beta receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsThomas, C. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural linkage between ligand discrimination and receptor activation by type I interferons.
Authors: Thomas, C. / Moraga, I. / Levin, D. / Krutzik, P.O. / Podoplelova, Y. / Trejo, A. / Lee, C. / Yarden, G. / Vleck, S.E. / Glenn, J.S. / Nolan, G.P. / Piehler, J. / Schreiber, G. / Garcia, K.C.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon alpha/beta receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8632
Polymers35,6421
Non-polymers2211
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.090, 86.180, 91.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interferon alpha/beta receptor 1 / Interferon-alpha/beta receptor / IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor ...IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor family 2 member 1 / CRF2-1 / Type I interferon receptor 1


Mass: 35641.816 Da / Num. of mol.: 1 / Fragment: UNP Residues 30-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR1, IFNAR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17181
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 298 K
Details: 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→19.486 Å / Num. obs: 55817 / % possible obs: 98.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 5.3 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 74.8 / % possible all: 98.3

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Processing

Software
NameClassification
Blu-Icedata collection
autoSHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→19.486 Å / σ(F): 1.49 / Stereochemistry target values: ML
Details: ANOMALOUS SCATTERER GROUP USED FOR ATOM SE WITH FP = -5.4570 AND FDP = 4.9472
RfactorNum. reflection% reflection
Rfree0.234 2784 4.99 %
Rwork0.21 --
obs-55817 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.27 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-0 Å2
2--7.31 Å20 Å2
3----10.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 14 145 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232269
X-RAY DIFFRACTIONf_angle_d1.3453093
X-RAY DIFFRACTIONf_dihedral_angle_d15.731801
X-RAY DIFFRACTIONf_chiral_restr0.128348
X-RAY DIFFRACTIONf_plane_restr0.007386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96780.34642800.29455301X-RAY DIFFRACTION98
1.9678-2.04650.28162750.25575278X-RAY DIFFRACTION98
2.0465-2.13960.24942780.22485275X-RAY DIFFRACTION98
2.1396-2.25220.2472780.22275270X-RAY DIFFRACTION99
2.2522-2.39310.28522820.23875352X-RAY DIFFRACTION99
2.3931-2.57750.26882810.24265329X-RAY DIFFRACTION99
2.5775-2.83610.25952770.2265321X-RAY DIFFRACTION99
2.8361-3.24490.22592830.21595340X-RAY DIFFRACTION100
3.2449-4.0820.23142790.19485373X-RAY DIFFRACTION100
4.082-19.48660.19522710.18775194X-RAY DIFFRACTION97
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)
10.62150.4850.57180.81430.9510.5794-0.03590.26090.02450.06870.00040.07980.19660.0422-0.00060.272-0.0406-0.01690.2881-0.02530.21449.714-12.38891.0721
21.03840.31970.05840.84650.90052.49490.02330.0685-0.04990.15660.05290.04980.19530.2179-0.00280.1627-0.0026-0.00570.1373-0.02320.2093-7.709-29.337-36.722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 7:98
2X-RAY DIFFRACTION2chain A and resid 99:299

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