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- PDB-3hhc: Interferon-lambda is functionally an interferon but structurally ... -

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Basic information

Entry
Database: PDB / ID: 3hhc
TitleInterferon-lambda is functionally an interferon but structurally related to the IL-10 family
ComponentsInterleukin-28B
KeywordsCYTOKINE / Interferon / IL-22 / antiviral / Antiviral defense / Secreted
Function / homology
Function and homology information


type III interferon-mediated signaling pathway / negative regulation of viral genome replication / Interleukin-20 family signaling / cell surface receptor signaling pathway via JAK-STAT / cytokine activity / cellular response to virus / positive regulation of immune response / defense response to virus / signaling receptor binding / innate immune response ...type III interferon-mediated signaling pathway / negative regulation of viral genome replication / Interleukin-20 family signaling / cell surface receptor signaling pathway via JAK-STAT / cytokine activity / cellular response to virus / positive regulation of immune response / defense response to virus / signaling receptor binding / innate immune response / extracellular space / extracellular region
Similarity search - Function
Interferon lambda / Interferon lambda / Interferon lambda superfamily / Interleukin-28A / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Interferon lambda-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsGad, H.H. / Hamming, O.J. / Hartmann, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Interferon-{lambda} Is Functionally an Interferon but Structurally Related to the Interleukin-10 Family
Authors: Gad, H.H. / Dellgren, C. / Hamming, O.J. / Vends, S. / Paludan, S.R. / Hartmann, R.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification ..._diffrn_source.pdbx_synchrotron_site / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-28B
B: Interleukin-28B
C: Interleukin-28B
D: Interleukin-28B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,39539
Polymers86,9544
Non-polymers4,44235
Water1,02757
1
A: Interleukin-28B
C: Interleukin-28B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,39625
Polymers43,4772
Non-polymers2,91923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-15 kcal/mol
Surface area14950 Å2
MethodPISA
2
B: Interleukin-28B
D: Interleukin-28B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,00014
Polymers43,4772
Non-polymers1,52312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-9 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.118, 91.118, 150.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Interleukin-28B / IL-28B / IL-28C / Interferon lambda-3 / IFN-lambda-3 / Interferon lambda-4 / IFN-lambda-4 / Cytokine ZCYTO22


Mass: 21738.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL28B, IFNL3, IFNL4, IL28C, ZCYTO22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IZI9
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 28 % w/v PEG 4000, 200 mM ammonium sulfate, 3 % v/v isopropyl alcohol , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, Hamburg X1210.907
SYNCHROTRONMAX II I911-321.65
SYNCHROTRONMAX II I911-330.9
Detector
TypeIDDetector
MARMOSAIC 225 mm CCD1CCD
MARMOSAIC 225 mm CCD2CCD
MARMOSAIC 225 mm CCD3CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9071
21.651
30.91
ReflectionResolution: 2.8→25 Å / Num. obs: 39210 / % possible obs: 91.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.062 / Χ2: 1.062 / Net I/σ(I): 24.389
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.693.70.30820640.86348.4
2.69-2.84.10.29630850.8172
2.8-2.934.80.24940740.8394.1
2.93-3.085.90.16142690.88199.6
3.08-3.276.40.10542710.9699.9
3.27-3.536.40.0843101.09599.9
3.53-3.886.40.06842561.19899.8
3.88-4.446.40.0643091.05999.8
4.44-5.586.40.06842891.35799.8
5.58-256.30.04542831.17999.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→23.863 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.718 / SU ML: 1.23 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.314 1226 6.77 %
Rwork0.261 --
obs0.265 18103 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.646 Å2 / ksol: 0.268 e/Å3
Displacement parametersBiso max: 330.34 Å2 / Biso mean: 94.783 Å2 / Biso min: 24.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.908 Å20 Å2-0 Å2
2--5.908 Å2-0 Å2
3----11.815 Å2
Refinement stepCycle: LAST / Resolution: 2.8→23.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 35 57 4506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034500
X-RAY DIFFRACTIONf_angle_d0.6626068
X-RAY DIFFRACTIONf_chiral_restr0.044715
X-RAY DIFFRACTIONf_plane_restr0.002780
X-RAY DIFFRACTIONf_dihedral_angle_d14.8521697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.9120.341420.2651793193597
2.912-3.0440.3771330.27318591992100
3.044-3.2040.3831410.26918652006100
3.204-3.4050.3711330.2761851198499
3.405-3.6670.361260.2631837196397
3.667-4.0340.3231310.2421847197898
4.034-4.6140.3141360.2371900203699
4.614-5.7990.2931370.25219252062100
5.799-23.8640.2451470.2492000214799
Refinement TLS params.Method: refined / Origin x: -15.0892 Å / Origin y: 27.2206 Å / Origin z: 64.5259 Å
111213212223313233
T0.6101 Å20.0139 Å20.2858 Å2-0.2795 Å2-0.0391 Å2--0.2512 Å2
L1.2865 °20.71 °2-0.0605 °2-1.936 °2-0.6847 °2--0.336 °2
S-0.3253 Å °0.1412 Å °-0.2923 Å °-0.9128 Å °0.1924 Å °-0.3095 Å °0.2925 Å °0.165 Å °0.1669 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 163
2X-RAY DIFFRACTION1allB4 - 163
3X-RAY DIFFRACTION1allC2 - 163
4X-RAY DIFFRACTION1allD14 - 152
5X-RAY DIFFRACTION1allB - C21 - 176
6X-RAY DIFFRACTION1allB1 - 187
7X-RAY DIFFRACTION1allC35 - 216

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