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- PDB-6sff: mouse Interleukin-12 subunit beta - p80 homodimer in space group I41 -

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Basic information

Entry
Database: PDB / ID: 6sff
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group I41
ComponentsInterleukin-12 subunit beta
KeywordsCYTOKINE / homodimer / antagonist / fibronectin / secreted glycoprotein
Function / homology
Function and homology information


Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / natural killer cell activation / T-helper cell differentiation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / negative regulation of protein secretion / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / positive regulation of defense response to virus by host / positive regulation of interleukin-12 production / : / cytokine activity / endosome lumen / negative regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to type II interferon / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / cell population proliferation / cell surface receptor signaling pathway / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. ...Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-12 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders12S0519N Belgium
Research Foundation - FlandersG0B4918N Belgium
Research Foundation - FlandersG0E1516N Belgium
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.
Authors: Kozak, S. / Bloch, Y. / De Munck, S. / Mikula, A. / Bento, I. / Savvides, S.N. / Meijers, R.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5073
Polymers39,3991
Non-polymers1,1082
Water59433
1
A: Interleukin-12 subunit beta
hetero molecules

A: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0146
Polymers78,7972
Non-polymers2,2174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3880 Å2
ΔGint13 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.876, 85.876, 107.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-518-

HOH

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Components

#1: Protein Interleukin-12 subunit beta / IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40


Mass: 39398.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues [1-22] encode the signal peptide which is cleaved during translation of the protein.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S GlycoDelete / Production host: Homo sapiens (human) / References: UniProt: P43432
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 6.5
Details: 120 mM monosaccharides, 50 mM Imidazole, 50 mM MES, pH6.5, 20% Ethylene glycol, 10 % PEG 8000 (MORPHEUS 1, F2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→67.41 Å / Num. obs: 15233 / % possible obs: 99.7 % / Redundancy: 8.11 % / Biso Wilson estimate: 60.25 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.125 / Net I/σ(I): 12.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7.17-67.418.1547.8259210.037100
5.08-7.178.3432.6310450.9980.06299.9
4.15-5.088.1829.9513590.9980.067100
3.6-4.158.2220.5915830.9970.098100
3.22-3.68.3713.2617950.9920.155100
2.94-3.228.336.3819910.9740.313100
2.72-2.948.2821460.9140.57799.9
2.55-2.728.341.8523030.8110.9999.9
2.4-2.557.160.9724190.5551.55198.5

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.16_3549refinement
XDS20190315data reduction
XDS20190315data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mj3

5mj3


Resolution: 2.4→67.14 Å / SU ML: 0.4403 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.887
RfactorNum. reflection% reflection
Rfree0.2645 1513 9.94 %
Rwork0.2293 --
obs0.2329 15218 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→67.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 73 33 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332432
X-RAY DIFFRACTIONf_angle_d0.56743308
X-RAY DIFFRACTIONf_chiral_restr0.0419384
X-RAY DIFFRACTIONf_plane_restr0.0036413
X-RAY DIFFRACTIONf_dihedral_angle_d2.35041973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.43651330.35951205X-RAY DIFFRACTION96.68
2.48-2.570.42551440.36931243X-RAY DIFFRACTION99.93
2.57-2.670.41921380.34351221X-RAY DIFFRACTION99.71
2.67-2.790.38771330.3021253X-RAY DIFFRACTION99.78
2.79-2.940.30281450.27221235X-RAY DIFFRACTION99.93
2.94-3.120.36071320.26711261X-RAY DIFFRACTION100
3.12-3.360.31741400.25781254X-RAY DIFFRACTION100
3.36-3.70.27161320.22341245X-RAY DIFFRACTION100
3.7-4.240.22261410.20611249X-RAY DIFFRACTION100
4.24-5.340.20631360.17871258X-RAY DIFFRACTION99.93
5.34-67.140.22071390.20751281X-RAY DIFFRACTION99.86

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