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- PDB-6sp3: mouse Interleukin-12 subunit beta - p80 homodimer in space group ... -

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Basic information

Entry
Database: PDB / ID: 6sp3
Titlemouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 1
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 granulocyte macrophage colony-stimulating factor production / positive regulation of natural killer cell proliferation / cytokine receptor activity / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / defense response to protozoan / 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 / defense response to virus / cellular response to lipopolysaccharide / cell population proliferation / defense response to Gram-negative bacterium / 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: 3 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: To Be Published
Title: Around she goes: the structure of mouse Interleukin-12 p80
Authors: Bloch, Y. / Savvides, S.N.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)80,9795
Polymers78,7972
Non-polymers2,1813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Assembly is present in multiple crystal forms. SEC MALLS data identifies a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint24 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.800, 176.140, 54.370
Angle α, β, γ (deg.)90.000, 108.963, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYR(chain 'A' and (resid 23 through 54 or (resid 55...AA23 - 8823 - 88
12HISHISGLNGLN(chain 'A' and (resid 23 through 54 or (resid 55...AA91 - 27591 - 275
13GLYGLYPROPRO(chain 'A' and (resid 23 through 54 or (resid 55...AA287 - 330287 - 330
24METMETTYRTYR(chain 'B' and (resid 23 through 89 or resid 91...BB23 - 8823 - 88
25HISHISGLNGLN(chain 'B' and (resid 23 through 89 or resid 91...BB91 - 27591 - 275
26GLYGLYPROPRO(chain 'B' and (resid 23 through 89 or resid 91...BB287 - 330287 - 330

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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: Residues [1-22] form the signal peptide and are most likely cleaved off during protein maturation.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S MGat1 -/- 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.: 2
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: obtained synthetically / Formula: Cl
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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% MPD, 10% PEG6000, 100mM HEPES pH7.5 (Crystal screen HT condition 78)
Temp details: thermostatted incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.99→58.714 Å / Num. obs: 19059 / % possible obs: 98.9 % / Redundancy: 4.13 % / Biso Wilson estimate: 100.061 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.078 / Net I/σ(I): 12.59
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
8.86-58.7143.8843.567440.9990.0291
6.32-8.863.9431.8613340.9990.0411
5.17-6.324.0424.7616900.9980.0511
4.48-5.174.1521.619740.9980.0621
4.01-4.484.1514.8222850.9970.0881
3.66-4.014.178.9524810.990.1581
3.39-3.664.355.2626920.9710.291
3.18-3.394.022.4329020.8920.611
2.99-3.184.161.1129570.6461.3581

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
PHENIX1.16_3549refinement
XDS20170615data reduction
XDS20170615data scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6sff

6sff


Resolution: 3→50.88 Å / SU ML: 0.546 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9544
RfactorNum. reflection% reflection
Rfree0.2674 950 5 %
Rwork0.2394 --
obs0.2407 19007 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 120.57 Å2
Refinement stepCycle: LAST / Resolution: 3→50.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 145 0 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274891
X-RAY DIFFRACTIONf_angle_d0.65386670
X-RAY DIFFRACTIONf_chiral_restr0.0442777
X-RAY DIFFRACTIONf_plane_restr0.0025840
X-RAY DIFFRACTIONf_dihedral_angle_d2.38153437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.491380.45872521X-RAY DIFFRACTION98.34
3.16-3.360.36941370.34022567X-RAY DIFFRACTION99.63
3.36-3.620.33971350.29312588X-RAY DIFFRACTION99.74
3.62-3.980.28551330.24572570X-RAY DIFFRACTION99.89
3.98-4.560.26571370.21292601X-RAY DIFFRACTION99.78
4.56-5.740.18861360.1982586X-RAY DIFFRACTION99.71
5.74-50.880.26071340.22622624X-RAY DIFFRACTION99.64
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)
15.222198929964.13688767256-4.30303799634.93899413734-4.20920007444.489432253710.101195469125-0.583735712317-0.4041476420930.388502167104-0.427068200984-0.718732218914-0.2450885000430.604514859660.001159017765750.910945844166-0.0114362866869-0.1202446860530.8622139003740.07376181490390.9989922638650.93200882762732.68438156017.00156998983
27.46264154101-0.955749215789-0.4809587989360.9453774133161.732871878244.16662710774-0.293389288993-0.960190247990.6607518835150.5273069637420.26247481530.659766904121-0.810700984695-1.07077391929-0.06735860509811.468595731210.3995536908870.1746425082321.213597176260.314032682351.57488733197-33.684746871118.798839927427.5462283848
39.0426611878-4.68576289709-2.061192127442.452905762221.168676633611.03112201930.1128086599790.2053881098580.0854213296938-0.124619765787-0.162359110589-0.1694127990.02907701910280.02257792884960.1487641496540.9917015831070.0778922110051-0.05879700639510.874396672690.03087568158020.8086027766754.50955830685-26.581935896118.2007822468
48.699401050961.40795597606-2.658196635964.62018349835-1.361900510766.50442792602-0.227823236969-0.744371921357-0.5205485632960.8398184071350.2446226191110.7017678070620.800964410836-0.775630090493-0.248689948611.148221623640.03677060546910.005011129957930.9538763219260.1221341147710.937488276718-29.419058276-10.926189659237.9737450481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:230 or resid 350:355)
2X-RAY DIFFRACTION2chain A and resid 231:334
3X-RAY DIFFRACTION3chain B and (resid 1:230 or resid 350:355)
4X-RAY DIFFRACTION4chain B and resid 231:334

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