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- PDB-9cym: Structure of LAG3 bound to the MHC class II molecule I-A(b) -

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Basic information

Entry
Database: PDB / ID: 9cym
TitleStructure of LAG3 bound to the MHC class II molecule I-A(b)
Components
  • Class-II-associated invariant chain peptide
  • H-2 class II histocompatibility antigen, A beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Secreted lymphocyte activation gene 3 protein
KeywordsIMMUNE 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 prostaglandin biosynthetic process / T cell selection / negative regulation of T cell activation / positive regulation of type 2 immune response / positive regulation of natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen / B cell affinity maturation / negative thymic T cell selection / host-mediated suppression of symbiont invasion / protein antigen binding / MHC class II protein binding / MHC class II antigen presentation / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / positive thymic T cell selection / CD4 receptor binding / positive regulation of monocyte differentiation / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / cytokine receptor activity / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / nitric-oxide synthase binding / negative regulation of interleukin-2 production / regulation of macrophage activation / natural killer cell mediated cytotoxicity / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / immunoglobulin mediated immune response / : / response to type II interferon / toxic substance binding / regulation of immune response / positive regulation of chemokine production / positive regulation of B cell proliferation / MHC class II antigen presentation / protein folding chaperone / multivesicular body / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / T cell activation / 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 / MHC class II protein complex / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / cellular response to type II interferon / peptide antigen binding / positive regulation of interleukin-6 production / positive regulation of fibroblast proliferation / transmembrane signaling receptor activity / MHC class II protein complex binding / endocytic vesicle membrane / late endosome / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / lysosome / early endosome / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / protein stabilization / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Interleukin-1 receptor family / Thyroglobulin type-1 repeat signature. ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Interleukin-1 receptor family / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class II histocompatibility antigen gamma chain / H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain / Lymphocyte activation gene 3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsMing, Q. / Antfolk, D. / Tran, T.H. / Luca, V.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentBankhead-Coley grant from the Florida Department of Health, Grant # 22B07 United States
Rita Allen Foundation United States
CitationJournal: 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
DepositionAug 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 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
L: Secreted lymphocyte activation gene 3 protein
A: H-2 class II histocompatibility antigen, A-B alpha chain
P: Class-II-associated invariant chain peptide
B: H-2 class II histocompatibility antigen, A beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9368
Polymers72,0514
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.652, 187.652, 124.057
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein Secreted lymphocyte activation gene 3 protein / sLAG-3


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
#2: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


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 Class-II-associated invariant chain peptide / CLIP


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 H-2 class II histocompatibility antigen, A beta chain


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 / 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.: 4 / Source method: obtained synthetically / 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
Has ligand of interestY
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: 4.19 Å3/Da / Density % sol: 70.62 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.84-3.942.6765150.9462.8671
3.94-4.055.5818940.0965.9371
4.05-4.174.1798810.1444.4091
4.17-4.293.1818400.3373.3471
4.29-4.431.9188280.5632.0181
4.43-4.591.4358110.6521.5121
4.59-4.761.0827610.7451.141
4.76-4.960.8657510.8130.9121
4.96-5.180.6877200.8630.7241
5.18-5.430.5796850.9250.6121
5.43-5.720.5326560.8930.5631
5.72-6.070.3866320.930.4121
6.07-6.490.3115950.9730.3281
6.49-7.010.2035470.9870.2141
7.01-7.680.1225150.9960.1291
7.68-8.590.074720.9980.0741
8.59-9.910.03742010.0391
9.91-12.140.02536110.0271
12.14-17.170.02130110.0221

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.3068 609 5.02 %
Rwork0.2595 11534 -
obs0.2619 12143 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 234.31 Å2
Refinement stepCycle: LAST / Resolution: 3.84→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 56 0 4779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194911
X-RAY DIFFRACTIONf_angle_d0.53296715
X-RAY DIFFRACTIONf_chiral_restr0.0443748
X-RAY DIFFRACTIONf_plane_restr0.0039876
X-RAY DIFFRACTIONf_dihedral_angle_d10.7191808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.84-4.230.5671260.53712364X-RAY DIFFRACTION80.3
4.23-4.840.39721570.34172981X-RAY DIFFRACTION99.97
4.84-6.090.30661590.29823021X-RAY DIFFRACTION100
6.09-38.610.25461670.19083168X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -2.22828682959 Å / Origin y: -73.0049892443 Å / Origin z: 5.13767024764 Å
111213212223313233
T1.66228804689 Å2-0.0581417559681 Å20.0698055288122 Å2-1.14851553555 Å2-0.0513280963676 Å2--1.52639491682 Å2
L2.75156266151 °20.0953108426036 °2-1.23539201263 °2-1.81761987596 °20.546222063647 °2--1.89798340015 °2
S-0.00467488682181 Å °0.339688444188 Å °-0.27040036242 Å °-0.422649662912 Å °0.128859116704 Å °-0.285030861902 Å °0.206114016416 Å °-0.216250777101 Å °-0.143431807543 Å °
Refinement TLS groupSelection details: all

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