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- PDB-3oq3: Structural Basis of Type-I Interferon Sequestration by a Poxvirus... -

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Basic information

Entry
Database: PDB / ID: 3oq3
TitleStructural Basis of Type-I Interferon Sequestration by a Poxvirus Decoy Receptor
Components
  • IFN-alpha/beta binding protein C12R
  • Interferon alpha-5
KeywordsCYTOKINE/VIRAL PROTEIN / Ectromelia / Mousepox Virus / Moscow strain / Cytokine decoy Receptor / Virus/Viral protein / Type-1 Interferon / Soluble a/b-IFNR / Viral immune evasion / Immunoglobulin Domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Immunoglobulin-like / IFN-alpha/beta binding protein / IFN-alpha / extracellular / secreted / CYTOKINE-VIRAL PROTEIN complex
Function / homology
Function and homology information


Regulation of IFNA/IFNB signaling / type I interferon receptor binding / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / T cell activation involved in immune response / response to exogenous dsRNA / B cell proliferation / humoral immune response / B cell differentiation ...Regulation of IFNA/IFNB signaling / type I interferon receptor binding / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / T cell activation involved in immune response / response to exogenous dsRNA / B cell proliferation / humoral immune response / B cell differentiation / cytokine activity / cytokine-mediated signaling pathway / defense response to virus / adaptive immune response / extracellular space
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interleukin-1 receptor family / Growth Hormone; Chain: A; - #10 / Immunoglobulin domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin ...Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interleukin-1 receptor family / Growth Hormone; Chain: A; - #10 / Immunoglobulin domain / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Interferon alpha-5 / IFN-alpha/beta binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Ectromelia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/molecular replacement / Resolution: 2.1 Å
AuthorsFremont, D.H. / Lee, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structural Basis of Type-I Interferon Sequestration by a Poxvirus Decoy Receptor
Authors: Fremont, D.H. / Lee, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon alpha-5
B: IFN-alpha/beta binding protein C12R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,55612
Polymers56,6122
Non-polymers94410
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-55 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.840, 75.900, 182.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Interferon alpha-5 / IFN-alpha-5


Mass: 18985.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifna5 / Plasmid: pET23B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P07349
#2: Antibody IFN-alpha/beta binding protein C12R / Interferon alpha/beta receptor / Soluble interferon-alpha/beta receptor


Mass: 37626.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Strain: Moscow / Gene: C12R, EVM166 / Plasmid: pET23B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9JFS5

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Non-polymers , 6 types, 371 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 17% 2-methyl-2,4-pentanediol (MPD), 2% polyethylene glycol 6000 (PEG 6000), and 100 mM NaOAc (pH 5.3), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→45.68 Å / Num. all: 73486 / Num. obs: 66438 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.29 % / Rmerge(I) obs: 0.086 / Χ2: 0.95 / Net I/σ(I): 6.7 / Scaling rejects: 1827
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.183.240.3352.52303570761.1692.5
2.18-2.263.180.3952.82298470711.3192.4
2.26-2.373.260.26132355172061.0494.2
2.37-2.493.230.2083.62365073070.9895.6
2.49-2.653.220.1654.42409574620.9497.2
2.65-2.853.260.1445.42464675150.997.9
2.85-3.143.340.1026.82530875430.898.3
3.14-3.593.320.0799.42469973560.8196.3
3.59-4.523.210.06112.52379773090.8795.2
4.52-45.683.620.052152783176410.7799.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.7LDzdata processing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
d*TREKdata reduction
d*TREKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD/molecular replacement
Starting model: PDB ENTRY 1ITF

1itf


Resolution: 2.1→43.072 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 3518 4.9 %RANDOM
Rwork0.2028 ---
obs0.2044 71824 93.8 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.467 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 99.66 Å2 / Biso mean: 35.891 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--5.5661 Å2-0 Å20 Å2
2---0.9441 Å20 Å2
3---6.5102 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 56 361 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074112
X-RAY DIFFRACTIONf_angle_d1.0035562
X-RAY DIFFRACTIONf_chiral_restr0.063620
X-RAY DIFFRACTIONf_plane_restr0.005711
X-RAY DIFFRACTIONf_dihedral_angle_d13.1521537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1750.30433840.26926364674888
2.175-2.26210.30773200.26516435675588
2.2621-2.3650.26662960.26076606690290
2.365-2.48970.31843740.2436723709793
2.4897-2.64570.28023310.22616980731195
2.6457-2.84990.24453530.20417028738196
2.8499-3.13660.20333520.20257102745497
3.1366-3.59030.22873840.19136916730096
3.5903-4.52270.20083550.1696921727695
4.5227-43.08120.21433690.18727231760099

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