+Open data
-Basic information
Entry | Database: PDB / ID: 9cym | |||||||||
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Title | Structure of LAG3 bound to the MHC class II molecule I-A(b) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / LAG3 / MHC class II / Immune checkpoint / T cell | |||||||||
Function / homology | Function and homology information positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / plasmacytoid dendritic cell activation / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / plasmacytoid dendritic cell activation / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / negative regulation of regulatory T cell differentiation / positive regulation of T-helper 1 type immune response / T cell activation involved in immune response / positive regulation of type 2 immune response / positive regulation of prostaglandin biosynthetic process / T cell selection / negative regulation of T cell activation / positive regulation of natural killer cell mediated cytotoxicity / negative thymic T cell selection / antigen processing and presentation of peptide antigen / protein antigen binding / negative regulation of viral entry into host cell / B cell affinity maturation / MHC class II protein binding / MHC class II antigen presentation / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / cytokine receptor activity / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / natural killer cell mediated cytotoxicity / regulation of macrophage activation / negative regulation of interleukin-2 production / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transport vesicle membrane / nitric-oxide synthase binding / cytokine binding / response to type II interferon / antigen processing and presentation / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / regulation of immune response / toxic substance binding / immunoglobulin mediated immune response / negative regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of chemokine production / protein folding chaperone / MHC class II antigen presentation / multivesicular body / lysosomal lumen / T cell activation / trans-Golgi network membrane / negative regulation of cell migration / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / lumenal side of endoplasmic reticulum membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / positive regulation of fibroblast proliferation / endocytic vesicle membrane / positive regulation of T cell activation / transmembrane signaling receptor activity / late endosome / MHC class II protein complex binding / late endosome membrane / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / protein stabilization / immune response / positive regulation of protein phosphorylation Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å | |||||||||
Authors | Ming, Q. / Antfolk, D. / Tran, T.H. / Luca, V.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for mouse LAG3 interactions with the MHC class II molecule I-A b. Authors: Ming, Q. / Antfolk, D. / Price, D.A. / Manturova, A. / Medina, E. / Singh, S. / Mason, C. / Tran, T.H. / Smalley, K.S.M. / Leung, D.W. / Luca, V.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cym.cif.gz | 315.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cym.ent.gz | 215.8 KB | Display | PDB format |
PDBx/mmJSON format | 9cym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cym_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 9cym_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9cym_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 9cym_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/9cym ftp://data.pdbj.org/pub/pdb/validation_reports/cy/9cym | HTTPS FTP |
-Related structure data
Related structure data | 9cylC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25711.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lag3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q61790 | ||||
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#2: Protein | Mass: 22026.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14434 | ||||
#3: Protein/peptide | Mass: 1733.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD74, DHLAG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04233 | ||||
#4: Protein | Mass: 22580.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14483 | ||||
#5: Sugar | ChemComp-NAG / Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.62 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.15 M Ammonium sulfate, 0.1 M Tris 8.0 and 15 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2024 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.84→38.61 Å / Num. obs: 12347 / % possible obs: 96.6 % / Redundancy: 10 % / Biso Wilson estimate: 133 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.21 / Net I/σ(I): 11.49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.84→38.61 Å / SU ML: 1.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 50.5982 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 234.31 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.84→38.61 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.22828682959 Å / Origin y: -73.0049892443 Å / Origin z: 5.13767024764 Å
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Refinement TLS group | Selection details: all |