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- PDB-8xrp: The Cryo-EM structure of IL-12, receptor subunit beta-1 and recep... -

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Basic information

Entry
Database: PDB / ID: 8xrp
TitleThe Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2 complex
Components
  • (Interleukin-12 receptor subunit beta- ...) x 2
  • (Interleukin-12 subunit ...) x 2
KeywordsCYTOKINE / IL-12 / IL-12RB1 / IL-12RB2 / receptor complex
Function / homology
Function and homology information


interleukin-27 binding / interleukin-12 beta subunit binding / late endosome lumen / interleukin-23-mediated signaling pathway / regulation of tyrosine phosphorylation of STAT protein / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of dendritic cell chemotaxis ...interleukin-27 binding / interleukin-12 beta subunit binding / late endosome lumen / interleukin-23-mediated signaling pathway / regulation of tyrosine phosphorylation of STAT protein / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of dendritic cell chemotaxis / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / 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 tissue remodeling / positive regulation of activation of Janus kinase activity / sexual reproduction / positive regulation of T-helper 1 type immune response / positive regulation of NK T cell activation / positive regulation of smooth muscle cell apoptotic process / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / positive regulation of memory T cell differentiation / interleukin-12 receptor complex / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / positive regulation of osteoclast differentiation / Interleukin-23 signaling / negative regulation of interleukin-17 production / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-35 Signalling / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / T-helper 1 type immune response / negative regulation of interleukin-10 production / cytokine binding / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of interleukin-10 production / positive regulation of cell adhesion / negative regulation of protein secretion / coreceptor activity / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / extrinsic apoptotic signaling pathway / 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 / regulation of cytokine production / positive regulation of interleukin-12 production / cytokine activity / negative regulation of smooth muscle cell proliferation / growth factor activity / response to virus / cellular response to virus / cytokine-mediated signaling pathway / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / 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 / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / response to lipopolysaccharide / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Interleukin-12 alpha / Interleukin-12 alpha subunit / Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site ...Interleukin-12 alpha / Interleukin-12 alpha subunit / Interleukin-12 beta / Interleukin-12 beta, central domain / Cytokine interleukin-12p40 C-terminus / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / 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 alpha / Interleukin-12 subunit beta / Interleukin-12 receptor subunit beta-1 / Interleukin-12 receptor subunit beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsChen, H.Q. / Wang, X.Q. / Ge, X.F. / Zeng, J.W. / Wang, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The Cryo-EM structure of IL-12/IL-12RB1-D1/IL-12RB2-D1-D3 complex
Authors: Chen, H.Q. / Wang, X.Q. / Ge, X.F. / Zeng, J.W. / Wang, J.W.
History
DepositionJan 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-12 subunit alpha
B: Interleukin-12 subunit beta
C: Interleukin-12 receptor subunit beta-2
D: Interleukin-12 receptor subunit beta-1
E: Interleukin-12 subunit alpha
F: Interleukin-12 subunit beta
G: Interleukin-12 receptor subunit beta-2
H: Interleukin-12 receptor subunit beta-1
I: Interleukin-12 subunit alpha
J: Interleukin-12 subunit beta
K: Interleukin-12 receptor subunit beta-2
L: Interleukin-12 receptor subunit beta-1
M: Interleukin-12 subunit alpha
N: Interleukin-12 subunit beta
O: Interleukin-12 receptor subunit beta-2
P: Interleukin-12 receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,82632
Polymers471,82616
Non-polymers5,00116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Interleukin-12 subunit ... , 2 types, 8 molecules AEIMBFJN

#1: Protein
Interleukin-12 subunit alpha / IL-12A / Cytotoxic lymphocyte maturation factor 35 kDa subunit / CLMF p35 / IL-12 subunit p35 / NK ...IL-12A / Cytotoxic lymphocyte maturation factor 35 kDa subunit / CLMF p35 / IL-12 subunit p35 / NK cell stimulatory factor chain 1 / NKSF1


Mass: 23781.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Interleukin-12 subunit alpha / Source: (gene. exp.) Homo sapiens (human) / Gene: IL12A, NKSF1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P29459
#2: Protein
Interleukin-12 subunit beta / IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40 / NK ...IL-12B / Cytotoxic lymphocyte maturation factor 40 kDa subunit / CLMF p40 / IL-12 subunit p40 / NK cell stimulatory factor chain 2 / NKSF2


Mass: 34811.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Interleukin-12 subunit beta / Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P29460

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Interleukin-12 receptor subunit beta- ... , 2 types, 8 molecules CGKODHLP

#3: Protein
Interleukin-12 receptor subunit beta-2 / IL-12 receptor subunit beta-2 / IL-12R subunit beta-2 / IL-12R-beta-2 / IL-12RB2


Mass: 34627.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Interleukin-12 receptor subunit beta-2 / Source: (gene. exp.) Homo sapiens (human) / Gene: IL12RB2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q99665
#4: Protein
Interleukin-12 receptor subunit beta-1 / IL-12 receptor subunit beta-1 / IL-12R subunit beta-1 / IL-12R-beta-1 / IL-12RB1 / IL-12 receptor ...IL-12 receptor subunit beta-1 / IL-12R subunit beta-1 / IL-12R-beta-1 / IL-12RB1 / IL-12 receptor beta component


Mass: 24736.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Interleukin-12 receptor subunit beta-1 / Source: (gene. exp.) Homo sapiens (human) / Gene: IL12RB1, IL12R, IL12RB / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P42701

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Sugars , 2 types, 16 molecules

#5: 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.: 4
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
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2 complex
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.485 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 8 / Details: 25mM Tris-HCl pH 8.0,150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HClTris-HCl1
2150 mMNaClNaCl1
SpecimenConc.: 1.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4547423
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 423691 / Symmetry type: POINT

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