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

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Basic information

Entry
Database: PDB / ID: 7pur
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 2
ComponentsInterleukin-12 subunit beta
KeywordsCYTOKINE / interleukin / homodimer
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 / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of smooth muscle cell apoptotic process ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of smooth muscle cell apoptotic process / positive regulation of T-helper 1 type immune response / T-helper cell differentiation / interleukin-12-mediated signaling pathway / positive regulation of NK T cell proliferation / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / cytokine receptor activity / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / response to UV-B / negative regulation of interleukin-10 production / defense response to protozoan / positive regulation of interleukin-17 production / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of protein secretion / cell surface receptor signaling pathway via JAK-STAT / T cell proliferation / positive regulation of defense response to virus by host / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / endosome lumen / growth factor activity / negative regulation of inflammatory response to antigenic stimulus / negative regulation of smooth muscle cell proliferation / cellular response to type II interferon / positive regulation of T cell mediated cytotoxicity / Golgi lumen / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / cell surface receptor signaling pathway / cell population proliferation / endoplasmic reticulum lumen / protein heterodimerization activity / cell surface / extracellular space / extracellular region / identical protein binding / membrane / 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 ...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: 3.9 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) 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
DepositionSep 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_diffrn_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1054
Polymers78,7972
Non-polymers2,3082
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, multiple other crystal forms also contain same assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.263, 158.334, 68.552
Angle α, β, γ (deg.)90.000, 100.214, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 2
Source method: isolated from a genetically manipulated source
Details: First 22 aminoacids are part of the secretion signal and are likely removed during translocation to the ER.
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: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 5% MPD, 10% PEG6000, 100mM TRIS pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.88→79.18 Å / Num. obs: 7714 / % possible obs: 97.8 % / Redundancy: 3.13 % / Biso Wilson estimate: 117.65 Å2 / CC1/2: 0.978 / Rrim(I) all: 0.325 / Net I/σ(I): 4.79
Reflection shellResolution: 3.88→4.11 Å / Redundancy: 3.13 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 1182 / CC1/2: 0.375 / Rrim(I) all: 1.9 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sff

6sff


Resolution: 3.9→39.62 Å / SU ML: 0.8238 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.9693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3237 767 10.01 %
Rwork0.2809 6895 -
obs0.2852 7662 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.3 Å2
Refinement stepCycle: LAST / Resolution: 3.9→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 155 0 4708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344818
X-RAY DIFFRACTIONf_angle_d0.8976573
X-RAY DIFFRACTIONf_chiral_restr0.0875784
X-RAY DIFFRACTIONf_plane_restr0.0033820
X-RAY DIFFRACTIONf_dihedral_angle_d14.98561740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.20.44191540.38241379X-RAY DIFFRACTION99.61
4.2-4.620.38631530.31131385X-RAY DIFFRACTION99.16
4.62-5.290.29891540.27421374X-RAY DIFFRACTION99.03
5.29-6.660.30891530.29551385X-RAY DIFFRACTION99.23
6.66-39.620.27861530.23191372X-RAY DIFFRACTION97.82
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)
15.610748368631.45052832887-3.378041783011.88740427642-1.579544780372.364801520130.147239677148-0.6095423102180.2487358031550.054303609637-0.119003885052-0.1823945490670.244437784780.1094441275310.02209468991931.25996806232-0.0958301057988-0.04985191125461.22314869931-0.04774648372281.1433747034-23.606264737-27.00858524572.737270233
23.73595038848-2.36353740594-2.002575126754.404541613210.5924062756717.552443149280.8388091525680.3145181226440.113907460182-0.235531663688-0.00414996541898-0.7454784364550.3045232061851.40754023574-0.9557526879261.67872137618-0.3520661869660.04952204320382.57624342097-0.4355497895721.775326923225.40672006069-11.247651576-23.976160171
33.93376672835-0.396808323287-1.873327221972.385663510370.8337503063765.367913657820.169106014930.06830541361920.001896380570570.179750485911-0.1851241910230.4162421227770.115259862731-0.4602844469110.0287226993611.47939235785-0.05096060527970.038620409091.218600339440.001777815736241.189402752261.2216177447826.504996646327.053956266
44.67402014378-0.955570351652-1.215363702351.705520683941.406588106261.96759068079-0.3032605419171.32407975760.0996719350289-1.028235147850.110886709560.1218507499530.372718984405-0.2047469414060.08500517821771.93904251971-0.374527206240.08872716830511.51939047512-0.03398462225211.4439610692420.419334766211.1165411767-4.94443442063
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resid 1:233 or resid 350:360)AA23 - 3551
22chain A and resid 234:334AA234 - 332212 - 293
33chain B and (resid 1:219 or resid 350:360)BB23 - 3571
44chain B and resid 220:333BB220 - 333198 - 301

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