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- PDB-3ux9: Structural insights into a human anti-IFN antibody exerting thera... -

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Basic information

Entry
Database: PDB / ID: 3ux9
TitleStructural insights into a human anti-IFN antibody exerting therapeutic potential for systemic lupus erythematosus
Components
  • Interferon alpha-1/13
  • ScFv antibody
KeywordsCYTOKINE/IMMUNE SYSTEM / five helices / long loop connecting helix / hydrophobic interactions / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


type I interferon receptor binding / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / T cell activation involved in immune response / TRAF6 mediated IRF7 activation / response to exogenous dsRNA / type I interferon-mediated signaling pathway / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling ...type I interferon receptor binding / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / T cell activation involved in immune response / TRAF6 mediated IRF7 activation / response to exogenous dsRNA / type I interferon-mediated signaling pathway / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / B cell differentiation / cytokine activity / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / blood coagulation / Factors involved in megakaryocyte development and platelet production / defense response to virus / adaptive immune response / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like ...Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon alpha-1/13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOuyang, S. / Zhao, L.X. / Liang, W. / Shaw, N. / Liu, Z.-J. / Liang, M.-F.
CitationJournal: J.Mol.Med. / Year: 2012
Title: Structural insights into a human anti-IFN antibody exerting therapeutic potential for systemic lupus erythematosus
Authors: Ouyang, S. / Gong, B. / Li, J.-Z. / Zhao, L.-X. / Wu, W. / Zhang, F.-S. / Sun, L. / Wang, S.-J. / Pan, M. / Li, C. / Liang, W. / Shaw, N. / Zheng, J. / Zhao, G.-P. / Wang, Y. / Liu, Z.-J. / Liang, M.-F.
History
DepositionDec 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon alpha-1/13
B: ScFv antibody
C: Interferon alpha-1/13
D: ScFv antibody


Theoretical massNumber of molelcules
Total (without water)93,9954
Polymers93,9954
Non-polymers00
Water72140
1
A: Interferon alpha-1/13
B: ScFv antibody


Theoretical massNumber of molelcules
Total (without water)46,9972
Polymers46,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-4 kcal/mol
Surface area15970 Å2
MethodPISA
2
C: Interferon alpha-1/13
D: ScFv antibody


Theoretical massNumber of molelcules
Total (without water)46,9972
Polymers46,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.225, 91.945, 43.633
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Interferon alpha-1/13 / interferon 1b / IFN-alpha-1/13 / Interferon alpha-D / LeIF D


Mass: 19681.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA1, IFNA13 / Plasmid: pMCSG 7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01562
#2: Antibody ScFv antibody


Mass: 27315.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: fully synthetic human antibody phage display library
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: magnesium acetate, 0.1M Tris (pH 8.5), 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 21650 / Num. obs: 21650 / % possible obs: 99.9 % / Observed criterion σ(F): 5.9 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.19 Å2
Reflection shellResolution: 2.75→2.82 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.54 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8132 / SU ML: 0.36 / σ(F): 0.2 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1085 5.01 %RANDOM
Rwork0.1832 ---
all0.1862 21650 --
obs0.1862 21650 94.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.373 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 191.69 Å2 / Biso mean: 62.0144 Å2 / Biso min: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1--14.2059 Å2-0 Å2-3.7768 Å2
2---14.3791 Å20 Å2
3----8.7382 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 0 40 5619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125695
X-RAY DIFFRACTIONf_angle_d1.37702
X-RAY DIFFRACTIONf_dihedral_angle_d19.8332019
X-RAY DIFFRACTIONf_chiral_restr0.105852
X-RAY DIFFRACTIONf_plane_restr0.005991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.92750.30961260.2389233786
2.9275-3.08180.29171180.2185242190
3.0818-3.27480.25941350.2039251294
3.2748-3.52750.24521390.1965256996
3.5275-3.88230.26061380.1837263898
3.8823-4.44350.21931430.1475267298
4.4435-5.59620.19691410.1425266899
5.5962-41.54440.21221450.177274899

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