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- PDB-3se4: human IFNw-IFNAR ternary complex -

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Basic information

Entry
Database: PDB / ID: 3se4
Titlehuman IFNw-IFNAR ternary complex
Components
  • Interferon alpha/beta receptor 1
  • Interferon alpha/beta receptor 2
  • Interferon omega-1
KeywordsIMMUNE SYSTEM RECEPTOR / Type I interferon signaling complex / extracellular space
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / regulation of cell cycle => GO:0051726 / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / response to interferon-beta / cellular response to interferon-alpha / natural killer cell activation involved in immune response / positive regulation of cellular respiration ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / regulation of cell cycle => GO:0051726 / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / response to interferon-beta / cellular response to interferon-alpha / natural killer cell activation involved in immune response / positive regulation of cellular respiration / response to interferon-alpha / positive regulation of peptidyl-serine phosphorylation of STAT protein / T cell activation involved in immune response / cytokine receptor binding / type I interferon-mediated signaling pathway / cytokine binding / B cell proliferation / response to exogenous dsRNA / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / B cell differentiation / cytokine activity / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / late endosome / defense response to virus / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / cell surface receptor signaling pathway / lysosome / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon omega-1 / Interferon alpha/beta receptor 1 / Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5001 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 10, 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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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
B: Interferon omega-1
C: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2284
Polymers91,0073
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-22 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.490, 93.490, 403.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Interferon alpha/beta receptor 1 / 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: 47629.965 Da / Num. of mol.: 1 / Fragment: IFNw (UNP Residues 28-436) / Mutation: N101Q
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: Protein Interferon omega-1 / Interferon alpha-II-1


Mass: 20482.746 Da / Num. of mol.: 1 / Fragment: UNP Residues 22-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNW1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P05000
#3: Protein Interferon alpha/beta receptor 2 / IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein ...IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein / Type I interferon receptor 2


Mass: 22894.078 Da / Num. of mol.: 1 / Fragment: UNP Residues 34-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Homo sapiens (human) / References: UniProt: P48551
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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

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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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 19% (w/v) PEG 3350, 100 mM Ammonium sulfate, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→19.845 Å / Num. obs: 13999 / % possible obs: 99.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 81.4 Å2 / Rsym value: 0.258 / Net I/σ(I): 10.8
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2 / Rsym value: 1.295 / % possible all: 99.7

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S98, 3S9D

3s98

3s9d


Resolution: 3.5001→19.845 Å / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 700 5 %
Rwork0.213 --
obs-13999 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.8 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 79.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.01 Å2-0 Å20 Å2
2---5.01 Å2-0 Å2
3---10.02 Å2
Refinement stepCycle: LAST / Resolution: 3.5001→19.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 14 0 4784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144912
X-RAY DIFFRACTIONf_angle_d1.7996688
X-RAY DIFFRACTIONf_dihedral_angle_d15.2131683
X-RAY DIFFRACTIONf_chiral_restr0.11767
X-RAY DIFFRACTIONf_plane_restr0.012847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.76870.31451350.25762574X-RAY DIFFRACTION100
3.7687-4.14480.33611360.2262590X-RAY DIFFRACTION100
4.1448-4.73740.24681380.17982623X-RAY DIFFRACTION100
4.7374-5.94190.27961400.22658X-RAY DIFFRACTION100
5.9419-19.84520.28841510.22112854X-RAY DIFFRACTION100
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)
11.155-0.19030.08552.0134-0.63743.04680.02690.1097-0.30540.04820.68570.50950.25460.12490.95670.61580.0461-0.29920.1373-0.14010.48699.0206-17.1629-22.8369
22.0452-1.2606-1.05442.93960.46490.5595-0.6948-0.5334-0.9431-0.3630.3691.01190.29920.6593-0.03510.50240.0065-0.21310.6232-0.04310.54766.6027-24.0895-24.945
30.07370.0074-0.1371.0382-0.02310.2628-0.52750.01880.05950.7017-0.2662-0.136-0.12550.5389-0.18380.53910.10220.01190.52090.19880.310811.835-23.1659-23.2178
40.29190.29340.42090.42170.38510.63210.8970.342-1.4241-0.5828-0.18540.12290.46620.29950.11540.4828-0.0487-0.25040.8994-0.08120.5710.6479-16.7231-27.3195
51.9864-0.0679-0.79020.11920.04590.31650.05990.2544-0.18220.07030.08330.5064-0.1367-0.3529-0.08540.55560.0169-0.18190.36750.00640.518419.1652-15.35146.6858
60.9419-0.01430.45661.1804-0.64680.9036-0.15070.15770.3634-0.01270.1613-0.2627-0.11710.0405-0.07890.3673-0.0469-0.2360.1573-0.09380.426920.9152-14.8185-1.2686
71.25410.4995-0.21840.7504-0.60671.2892-0.1103-0.00660.15210.27670.2704-0.2374-0.3092-0.1870.17970.2743-0.0133-0.22370.1357-0.06380.344723.7474-9.6633.8983
80.94670.2183-0.68780.2801-0.12920.4921-0.2224-0.30890.54930.17450.11920.1407-1.0457-0.0978-0.00510.56750.08670.02190.4571-0.14680.414724.3038-11.690222.8587
90.13570.1081-0.11810.7447-0.89311.06540.02670.00750.71070.3070.3213-0.3686-0.1590.1660.15120.44190.1269-0.22490.4531-0.14240.41639.7239-22.534725.016
100.0068-0.08070.01310.8271-0.34930.6012-0.1887-0.1824-0.4118-0.01740.24590.2420.87-0.00790.03120.511-0.0295-0.00960.509-0.00660.216132.4425-27.344616.7445
112.2209-0.95960.69820.52520.0251.1845-0.3014-0.5772-0.29530.55110.10680.12570.62810.3937-0.05110.45640.0316-0.13880.4322-0.0210.516337.5277-24.235219.7895
120.1352-0.4909-0.19192.60730.30620.46280.1988-0.6417-0.14010.2842-0.3659-0.41060.80390.04180.51990.7119-0.3004-0.0640.49660.37380.714549.1794-16.8348-4.1914
130.9821-0.69371.09781.49050.20984.53080.1358-0.70350.2483-0.0790.0495-0.96840.5680.06420.18720.32010.19660.03060.3512-0.16480.349346.5805-33.587-4.4099
140.56410.13320.08490.03140.02040.01310.1811-0.5579-0.10230.4239-0.2544-0.20140.0803-0.2522-0.02020.52510.0334-0.02550.2367-0.14430.201139.4298-49.0102-9.0862
150.55130.6451-0.43772.8354-0.36120.45040.01130.7152-0.271-0.8761-0.553-0.9496-0.2959-0.4478-0.12320.40340.12220.04240.6284-0.01530.377336.5884-35.9322-21.6119
161.50040.08721.0320.56130.19412.04640.48590.36130.126-0.0207-0.42920.6791-0.35340.17510.03740.287-0.0357-0.08970.4553-0.04720.496634.7179-28.8755-7.3593
170.1278-0.22220.00133.816-0.10890.2606-0.15290.07780.16270.88280.1008-0.4937-0.06990.34780.03040.2385-0.0013-0.0010.4902-0.03980.429238.8791-23.718-1.7972
181.9161-1.34910.17851.6649-0.78531.20840.06930.2685-0.2609-0.0734-0.19870.123-0.0807-0.1941-0.61620.0890.2702-0.47040.235-0.13010.34533.9567-35.2597-14.266
191.40521.7692-0.35813.4765-0.88610.82190.79610.0187-0.06510.7492-0.54660.06040.06250.30850.12440.34850.0167-0.00820.44210.01760.205159.1043-50.9821-13.3858
200.440.34850.21270.28980.41550.6199-0.1870.27260.0611-0.1411-0.06890.0674-0.115-0.0094-0.01490.3473-0.0030.00960.306-0.0440.359457.3802-48.8111-18.1469
210.8244-0.4333-0.1041.21170.67971.5149-0.4440.04050.829-0.21730.02470.0195-0.4145-0.0498-0.10730.2395-0.0601-0.04230.18950.00070.341874.4634-29.2585-9.8159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:40)
2X-RAY DIFFRACTION2chain 'A' and (resseq 41:60)
3X-RAY DIFFRACTION3chain 'A' and (resseq 61:81)
4X-RAY DIFFRACTION4chain 'A' and (resseq 82:98)
5X-RAY DIFFRACTION5chain 'A' and (resseq 99:120)
6X-RAY DIFFRACTION6chain 'A' and (resseq 121:149)
7X-RAY DIFFRACTION7chain 'A' and (resseq 150:191)
8X-RAY DIFFRACTION8chain 'A' and (resseq 192:208)
9X-RAY DIFFRACTION9chain 'A' and (resseq 209:236)
10X-RAY DIFFRACTION10chain 'A' and (resseq 237:262)
11X-RAY DIFFRACTION11chain 'A' and (resseq 263:302)
12X-RAY DIFFRACTION12chain 'B' and (resseq 2:9)
13X-RAY DIFFRACTION13chain 'B' and (resseq 10:22)
14X-RAY DIFFRACTION14chain 'B' and (resseq 23:31)
15X-RAY DIFFRACTION15chain 'B' and (resseq 32:51)
16X-RAY DIFFRACTION16chain 'B' and (resseq 52:80)
17X-RAY DIFFRACTION17chain 'B' and (resseq 81:117)
18X-RAY DIFFRACTION18chain 'B' and (resseq 118:161)
19X-RAY DIFFRACTION19chain 'C' and (resseq 9:30)
20X-RAY DIFFRACTION20chain 'C' and (resseq 31:126)
21X-RAY DIFFRACTION21chain 'C' and (resseq 127:205)

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