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- PDB-7r3n: mouse Interleukin-12 subunit beta - p80 homodimer in space group ... -

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Basic information

Entry
Database: PDB / ID: 7r3n
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 3
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 / positive regulation of defense response to virus by host / negative regulation of inflammatory response to antigenic stimulus / 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
PHOSPHATE ION / Interleukin-12 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Citation
Journal: To Be Published
Title: Around she goes: the structure of mouse Interleukin-12 p80
Authors: Bloch, Y. / Savvides, S.N.
#1: Journal: 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
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-12 subunit beta
B: Interleukin-12 subunit beta
C: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,43713
Polymers153,1304
Non-polymers3,3079
Water181
1
A: Interleukin-12 subunit beta
B: Interleukin-12 subunit beta
hetero molecules


  • defined by author
  • Evidence: light scattering, Homodimer, also present in PDB 6sff, 6smc, 6sp3 and 7pur.
  • 78.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)78,3477
Polymers76,5652
Non-polymers1,7825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint2 kcal/mol
Surface area34120 Å2
2
C: Interleukin-12 subunit beta
D: Interleukin-12 subunit beta
hetero molecules


  • defined by author
  • 78.1 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)78,0906
Polymers76,5652
Non-polymers1,5254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint6 kcal/mol
Surface area34690 Å2
Unit cell
Length a, b, c (Å)112.813, 65.165, 134.311
Angle α, β, γ (deg.)90.000, 98.093, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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: 38282.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues [1-22] encode a secretion signal which is should have been co-translationally removed.
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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.19 Å3/Da / Density % sol: 61.45 % / Description: parallelogram shaped plate
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6
Details: BCS screen, 0.2M sodium formate, 0.1M sodium phosphate pH 6.0, 17% PEG Smear Medium, 10% Glycerol. Cryoprotected with up to 27.5% PEG Smear Medium prior to vitrification.

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.1→111.67 Å / Num. obs: 35159 / % possible obs: 99.1 % / Redundancy: 4.64 % / Biso Wilson estimate: 89.24 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.16 / Net I/σ(I): 8.09
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 5551 / CC1/2: 0.526 / Rrim(I) all: 1.732 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.2_4158refinement
Coot0.9.4model building
PDB_EXTRACT3.27data extraction
XDS20210323data reduction
XDS20210323data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sff

6sff


Resolution: 3.16→61.03 Å / SU ML: 0.4417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 2005 6 %RANDOM
Rwork0.22 31435 --
obs0.2223 33440 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.81 Å2
Refinement stepCycle: LAST / Resolution: 3.16→61.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9657 0 214 1 9872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010410110
X-RAY DIFFRACTIONf_angle_d1.185213713
X-RAY DIFFRACTIONf_chiral_restr0.06331539
X-RAY DIFFRACTIONf_plane_restr0.0141733
X-RAY DIFFRACTIONf_dihedral_angle_d12.91053762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.230.38221400.3592204X-RAY DIFFRACTION97.46
3.23-3.320.36951420.32492233X-RAY DIFFRACTION99.12
3.32-3.420.30821440.2872248X-RAY DIFFRACTION99.29
3.42-3.530.31281410.26732211X-RAY DIFFRACTION98.82
3.53-3.660.31461410.25542204X-RAY DIFFRACTION99.2
3.66-3.80.28981440.25092222X-RAY DIFFRACTION98.79
3.8-3.980.31561400.2262250X-RAY DIFFRACTION99.46
3.98-4.190.22951440.20812253X-RAY DIFFRACTION99.75
4.19-4.450.21181410.18152227X-RAY DIFFRACTION99.5
4.45-4.790.22711460.18392265X-RAY DIFFRACTION99.38
4.79-5.270.23231430.17372237X-RAY DIFFRACTION99.33
5.27-6.030.241460.19062288X-RAY DIFFRACTION99.31
6.04-7.60.25211430.21852266X-RAY DIFFRACTION98.97
7.6-61.030.23161500.21782327X-RAY DIFFRACTION97.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.596057268732.861242866093.636479353843.262654803110.2476917922156.69411340446-0.4422297357830.7647719385150.326972707114-0.789607013130.591632200340.722789249727-0.0832034529011-0.718441153576-0.2547869211950.652785437833-0.0793084693127-0.1258020450510.6445187589090.1958772317891.02527737445-63.5111612843-0.87198515648955.1089703781
28.737075834231.39790224638-0.1858328937112.78113362584-0.8723089051942.60581489181-0.03348395579-0.03269675121960.55525304223-0.1466723308590.04565738124630.234825277768-0.03787936732050.273328906264-0.06322006804150.594990839380.0716918231118-0.06499123584050.14506336851-0.123928846570.826286932148-37.47068559931.2383957630267.9047107332
33.894525912411.162179751672.414981844022.423282348071.021569962128.255805093620.132931767782-1.00886993132-0.4667877951890.477404288949-0.0366945199079-0.1722504629760.9773170571190.642126206425-0.113883399860.64394088980.08670186818670.0193058154010.8131857178180.1127876363920.966527622459-13.0134066579-2.2047518392283.8681717122
42.088521485470.40897016343-0.3551190448290.7503953922010.9484977986676.96897538058-0.19934155160.731283639398-0.187082494564-0.378243657870.8180942757860.1360266655221.75246689818-0.0402800305713-0.2548969858171.946683818710.487423729323-0.179098869072.57300746025-0.1336930891741.09950311982-8.51213060729-2.633100225746.94853586035
51.737690697170.1971107123911.413583230144.194272590331.77039349668.804928365740.576089400021.3774067535-0.136670331521-1.09682965399-0.5272022788930.1755794541550.4494536614190.552889933820.1155579441810.9681266439370.224654152379-0.1744775480431.12564393857-0.04425703327810.688809583965-0.5976719519530.96399330448734.7695910313
66.64051454449-0.2747075190951.635751537685.75063746066-0.4216227918233.977018552160.04355777985080.39120476360.05033063150440.0141575096988-0.0910326462219-0.3234101176740.425108770450.03734531110020.06116154919890.602889017069-0.0592832314990.07927249640150.2385219343250.0310779903050.61824026574812.51975655518.520113794661.6845481531
71.771651244090.2771265762231.088114647140.631061122075-0.348670581333.762863197230.780564613967-0.943349829232-0.2021363091040.245431268333-0.419434884168-0.02313748010930.7559752801310.0362513666213-0.08357044000911.687322297760.0297013387245-0.07451571482752.504370001590.04963149737891.2179472860833.7281254601-2.0393130059221.1357569571
82.16235188964-0.3934529023481.213290653553.92336117198-0.6294727045527.212732613080.2123963524430.197230039586-0.1490525979760.5897198016750.0166926919036-0.144285461799-0.00774164318990.277310418468-0.1272375872861.187204471110.286613156057-0.04489408402352.302095423850.1260605541560.95523462452626.25597619771.25391058232-6.76880592293
91.49037253627-0.6431907197140.36129127942.380594089661.471508947915.36215903652-0.0484007152596-0.957993792883-0.0296535568472-0.446906291947-0.1061432854540.423094037991-0.41900961671.004098500170.06760749422131.127729002120.0488502863571-0.04229256409612.132847491750.1739722390780.99997608495313.95196117368.48922263222-33.5964105918
103.43791045363-1.34639208944-0.6292235746182.467185860861.619364114881.76700148066-0.358641546277-1.2746976669-0.4028398103970.4896560482390.394733571452-0.5082323724170.4589706898781.13178645066-0.1452770562190.9768409422890.0197964473483-0.0834102463191.88549595743-0.2416762248961.1474685208389.6633275629-0.664815990114-27.4313624823
116.40429709792-0.9257912763860.2286196057862.630117235760.05426531764813.97261458066-0.0843009620532-1.312000558320.1929207692460.2695409804210.1113624170170.0360141226720.04459371190370.0922041128835-0.05504584150630.729095200104-0.0355669659942-0.05500424025180.6759717303530.001609071642770.60416381421963.55149831.16681747547-40.0475643961
126.7831862957-1.112989744751.458391532666.17533907795-0.2587234467266.22347227138-0.130192526054-0.477321059298-0.450271649704-0.003619253739320.04080060188740.07360067526890.392930792396-0.0362269391118-0.1477519905590.629057673887-0.03742898133950.03640088666730.3409901099520.1882723894080.78942657585739.2031540649-2.69040470985-56.6876678109
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resid 23:109 or resid 350:355)AA - E23 - 3531
22chain A and resid 110:232AA110 - 23288 - 210
33chain A and resid 234:334AA234 - 333212 - 304
44chain B and (resid 23:109 or resid 350:355)BF - J23 - 3531
55chain B and resid 110:232BF110 - 23288 - 210
66chain B and resid 234:334BF234 - 334212 - 303
77chain C and (resid 23:109 or resid 350:355)CK - N23 - 3521
88chain C and resid 110:232CK110 - 23288 - 210
99chain C and resid 234:334CK234 - 333212 - 302
1010chain D and (resid 23:109 or resid 350:355)DD23 - 3531
1111chain D and resid 110:232DD110 - 23288 - 210
1212chain D and resid 234:334DD234 - 333212 - 305

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