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- PDB-8dgg: Structure of glycosylated LAG-3 homodimer -

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Basic information

Entry
Database: PDB / ID: 8dgg
TitleStructure of glycosylated LAG-3 homodimer
ComponentsLymphocyte activation gene 3 protein
KeywordsIMMUNE SYSTEM / Immune checkpoint receptor / homodimer / glycosylation
Function / homology
Function and homology information


plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / negative regulation of T cell activation / MHC class II protein binding / positive regulation of natural killer cell mediated cytotoxicity / MHC class II antigen presentation / natural killer cell mediated cytotoxicity / negative regulation of interleukin-2 production / regulation of immune response / T cell activation ...plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / negative regulation of T cell activation / MHC class II protein binding / positive regulation of natural killer cell mediated cytotoxicity / MHC class II antigen presentation / natural killer cell mediated cytotoxicity / negative regulation of interleukin-2 production / regulation of immune response / T cell activation / transmembrane signaling receptor activity / adaptive immune response / membrane => GO:0016020 / cell surface receptor signaling pathway / external side of plasma membrane / extracellular region
Similarity search - Function
Interleukin-1 receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-L-fucopyranose / Lymphocyte activation gene 3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 Å
AuthorsSilberstein, J.L. / Mathews, I.I. / Frank, J.A. / Chan, K.-W. / Fernandez, D. / Du, J. / Wang, J. / Kong, X.-P. / Cochran, J.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Structural basis for LAG-3 dimeric association and inhibition of T cell function
Authors: Silberstein, J.L. / Mathews, I.I. / Cochran, J.R.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lymphocyte activation gene 3 protein
B: Lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,97410
Polymers92,2452
Non-polymers2,7298
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, We also did size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.690, 97.670, 174.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Non-polymers , 2 types, 13 molecules AB

#1: Protein Lymphocyte activation gene 3 protein / LAG-3 / Activation-induced cytidine deaminase-linked autoimmunity protein / Aida


Mass: 46122.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lag3 / Production host: Homo sapiens (human) / References: UniProt: Q61790
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1M Tris, 0.05M L-Arginine, 0.05M L-Glutamic acid monosodium salt hydrate, 14% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2020 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.78→39.32 Å / Num. obs: 12782 / % possible obs: 99.8 % / Redundancy: 40.084 % / Biso Wilson estimate: 181.762 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.13 / Χ2: 0.803 / Net I/σ(I): 18.74 / Num. measured all: 512360 / Scaling rejects: 667
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.78-3.8842.4734.0421.48380568968960.5394.091100
3.88-3.9842.1032.7892.24386089179170.7752.823100
3.98-4.141.9671.9553.16369318808800.8681.978100
4.1-4.2341.3831.4054.38354658578570.9191.422100
4.23-4.3641.0380.9316.3336928218210.9510.943100
4.36-4.5240.4240.6169.21333098248240.9840.624100
4.52-4.6938.970.43211.72296177607600.9920.437100
4.69-4.8836.4830.315.08275817577560.9940.30499.9
4.88-5.141.4750.28916.91300287247240.9960.293100
5.1-5.3540.4030.24718.94278386896890.9960.25100
5.35-5.6440.3460.20321.85267096626620.9980.205100
5.64-5.9841.8660.17525.17265856356350.9980.177100
5.98-6.3941.7080.14827.61245665895890.9980.15100
6.39-6.940.6760.12732.03224535525520.9990.128100
6.9-7.5639.6950.10538.96208405255250.9990.107100
7.56-8.4537.5770.08444.34173234614610.9990.085100
8.45-9.7633.4050.07249.85140974244220.9990.07399.5
9.76-11.9536.5360.0754.97133723663660.9990.071100
11.95-16.9136.5160.06758.431040728528510.068100
16.91-39.3230.3290.0750.99488317816110.07190.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Manually corrected model from AlphaFold

Resolution: 3.78→39.32 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.909 / SU B: 48.037 / SU ML: 0.662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.782 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3153 640 5 %RANDOM
Rwork0.2553 ---
obs0.2584 12142 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 402.8 Å2 / Biso mean: 231.528 Å2 / Biso min: 141.34 Å2
Baniso -1Baniso -2Baniso -3
1--7.06 Å2-0 Å2-0 Å2
2--0.61 Å2-0 Å2
3---6.46 Å2
Refinement stepCycle: final / Resolution: 3.78→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 179 11 5049
Biso mean--274.7 181.99 -
Num. residues----631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0115192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164722
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.6567114
X-RAY DIFFRACTIONr_angle_other_deg0.2981.54511030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2021043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87810757
X-RAY DIFFRACTIONr_chiral_restr0.0440.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
LS refinement shellResolution: 3.78→3.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 45 -
Rwork0.358 844 -
all-889 -
obs--99.89 %

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