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- PDB-3s9d: binary complex between IFNa2 and IFNAR2 -

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Basic information

Entry
Database: PDB / ID: 3s9d
Titlebinary complex between IFNa2 and IFNAR2
Components
  • Interferon alpha-2
  • Interferon alpha/beta receptor 2
KeywordsSIGNALING PROTEIN/RECEPTOR / human / type I interferons / IFNa2 / IFNAR2 / sub-complex of the interferon signaling complex / SIGNALING PROTEIN-RECEPTOR complex
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / response to interferon-alpha / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytokine binding / response to exogenous dsRNA / humoral immune response / Regulation of IFNA/IFNB signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to interferon-beta / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / response to virus / Interferon alpha/beta signaling / cell-cell signaling / : / Factors involved in megakaryocyte development and platelet production / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / receptor complex / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / 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 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 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 / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon alpha-2 / Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9999 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 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 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
A: Interferon alpha-2
B: Interferon alpha/beta receptor 2
C: Interferon alpha-2
D: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4185
Polymers84,3824
Non-polymers351
Water6,485360
1
A: Interferon alpha-2
B: Interferon alpha/beta receptor 2


Theoretical massNumber of molelcules
Total (without water)42,1912
Polymers42,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-9 kcal/mol
Surface area16290 Å2
MethodPISA
2
C: Interferon alpha-2
D: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2273
Polymers42,1912
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-26 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 62.010, 88.080
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon alpha-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 19393.232 Da / Num. of mol.: 2 / Fragment: IFNa2 (UNP Residues 24-188) / Mutation: H57A, E58A, Q61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01563
#2: 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: 22797.992 Da / Num. of mol.: 2 / Fragment: UNP Residues 37-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48551
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K
Details: 20% (w/v) PEG 3350, 200 mM NaSCN, 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: 1.9999→19.897 Å / Num. obs: 61371 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9999→2.1 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 53.6 / % possible all: 99.1

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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 ENTRIES 3S8W, 2HYM, and 1RH2

3s8w

2hym

1rh2


Resolution: 1.9999→19.897 Å / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 3069 5 %
Rwork0.204 --
obs-61368 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.98 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å25.37 Å2
2--1.68 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9999→19.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 1 360 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165175
X-RAY DIFFRACTIONf_angle_d1.147030
X-RAY DIFFRACTIONf_dihedral_angle_d13.9381896
X-RAY DIFFRACTIONf_chiral_restr0.093810
X-RAY DIFFRACTIONf_plane_restr0.005876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.07130.28263030.24735763X-RAY DIFFRACTION99
2.0713-2.15420.28883040.24235763X-RAY DIFFRACTION99
2.1542-2.25210.28983040.23055779X-RAY DIFFRACTION99
2.2521-2.37060.26953070.2275831X-RAY DIFFRACTION99
2.3706-2.51890.27143050.21955788X-RAY DIFFRACTION99
2.5189-2.71290.25673060.2115828X-RAY DIFFRACTION100
2.7129-2.98510.27173090.2125861X-RAY DIFFRACTION100
2.9851-3.41520.21713080.19665852X-RAY DIFFRACTION100
3.4152-4.29560.21683080.1785855X-RAY DIFFRACTION99
4.2956-19.89870.19553150.19655979X-RAY DIFFRACTION99

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