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- PDB-7tze: Structure of murine LAG3 domains 1-2 -

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Basic information

Entry
Database: PDB / ID: 7tze
TitleStructure of murine LAG3 domains 1-2
ComponentsLymphocyte activation gene 3 protein
KeywordsIMMUNOSUPPRESSANT / Immune checkpoint / T cell / Ig-like fold
Function / homology
Function and homology information


plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / negative regulation of T cell activation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / MHC class II antigen presentation / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / T cell activation ...plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / negative regulation of T cell activation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / MHC class II antigen presentation / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / T cell activation / transmembrane signaling receptor activity / adaptive immune response / cell surface receptor signaling pathway / external side of plasma membrane / extracellular region
Similarity search - Function
Interleukin-1 receptor family / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lymphocyte activation gene 3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMing, Q. / Tran, T.H. / Luca, V.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133482 United States
V Foundation for Cancer Research United States
Rita Allen Foundation United States
CitationJournal: Nat.Immunol. / Year: 2022
Title: LAG3 ectodomain structure reveals functional interfaces for ligand and antibody recognition.
Authors: Ming, Q. / Celias, D.P. / Wu, C. / Cole, A.R. / Singh, S. / Mason, C. / Dong, S. / Tran, T.H. / Amarasinghe, G.K. / Ruffell, B. / Luca, V.C.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 13, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.5Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,3188
Polymers51,3092
Non-polymers1,0096
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.729, 92.534, 81.771
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 28 through 106 or (resid 107...
21(chain C and (resid 28 through 46 or (resid 47...

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
11GLUGLUARGARG(chain A and (resid 28 through 106 or (resid 107...AA28 - 1066 - 84
12SERSERSERSER(chain A and (resid 28 through 106 or (resid 107...AA10785
13GLUGLULEULEU(chain A and (resid 28 through 106 or (resid 107...AA28 - 2546 - 232
14GLUGLULEULEU(chain A and (resid 28 through 106 or (resid 107...AA28 - 2546 - 232
15GLUGLULEULEU(chain A and (resid 28 through 106 or (resid 107...AA28 - 2546 - 232
16GLUGLULEULEU(chain A and (resid 28 through 106 or (resid 107...AA28 - 2546 - 232
21GLUGLULEULEU(chain C and (resid 28 through 46 or (resid 47...CB28 - 466 - 24
22LYSLYSPROPRO(chain C and (resid 28 through 46 or (resid 47...CB47 - 4925 - 27
23LYSLYSLEULEU(chain C and (resid 28 through 46 or (resid 47...CB27 - 2545 - 232
24LYSLYSLEULEU(chain C and (resid 28 through 46 or (resid 47...CB27 - 2545 - 232
25LYSLYSLEULEU(chain C and (resid 28 through 46 or (resid 47...CB27 - 2545 - 232
26LYSLYSLEULEU(chain C and (resid 28 through 46 or (resid 47...CB27 - 2545 - 232

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Components

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


Mass: 25654.330 Da / Num. of mol.: 2 / Fragment: ectodomain
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: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40.27 Å / Num. obs: 32665 / % possible obs: 98.1 % / Redundancy: 3.846 % / Biso Wilson estimate: 56.032 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.099 / Χ2: 1.176 / Net I/σ(I): 8.28 / Num. measured all: 125635
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
2.05-2.183.9761.3280.9320446534151420.5361.53496.3
2.18-2.333.960.9561.3919790505749980.6791.10798.8
2.33-2.513.7840.5872.2917429469546060.8680.68598.1
2.51-2.753.7210.348415774434342390.9320.40897.6
2.75-3.083.9490.1957.715271389638670.9740.22699.3
3.08-3.553.8370.09713.8813226349334470.9920.11298.7
3.55-4.343.7290.05921.3710572290328350.9950.06997.7
4.34-6.133.8020.04925.868664229522790.9960.05799.3
6.13-40.273.5650.04127.214463128412520.9980.04897.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1-3660_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L1D, 3B43

4l1d

3b43


Resolution: 2.12→40.27 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1515 5.06 %
Rwork0.2121 28429 -
obs0.2133 29944 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.57 Å2 / Biso mean: 75.8027 Å2 / Biso min: 32.21 Å2
Refinement stepCycle: final / Resolution: 2.12→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 64 81 3372
Biso mean--81.9 63.57 -
Num. residues----416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1262X-RAY DIFFRACTION14.12TORSIONAL
12C1262X-RAY DIFFRACTION14.12TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.180.41961410.37892560270199
2.18-2.260.35391350.35462604273999
2.26-2.350.3671390.33442580271999
2.35-2.460.32771150.30282560267598
2.46-2.590.34011330.29172539267296
2.59-2.750.31921410.27732600274199
2.75-2.960.26781670.25162561272899
2.96-3.260.27971330.23232619275299
3.26-3.730.24111630.19652515267897
3.73-4.70.18581220.16232638276099
4.7-40.270.16051260.1732653277998
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)
14.24183.44593.60158.09245.41836.2217-0.0886-0.3290.3071-0.5172-0.2120.3355-0.26-0.23350.18230.55560.04260.05430.6796-0.1680.5717-2.488533.035836.4481
24.88151.45541.6796.35750.45765.2125-0.057-0.6042-0.23110.18810.01010.0162-0.1455-0.26120.080.33750.05870.0320.49540.0190.3496-11.29864.088522.9225
34.4088-2.54080.22837.6996-1.63137.03540.28340.419-0.7407-0.4295-0.06150.95230.6664-0.6595-0.19660.3868-0.05750.0050.3629-0.00020.7983-44.056521.6454-9.3707
48.5861-1.32174.38723.0865-1.02269.4877-0.4159-1.26530.65650.83850.2066-0.1966-1.15580.85460.35290.6596-0.04860.05190.48660.02880.674-37.536836.01690.8314
52.1986-2.47021.60594.2889-3.05262.19160.33921.6210.1261-0.68360.36460.0994-0.57060.36130.17521.02180.0225-0.00241.08590.01761.3959-38.590531.5465-20.6327
66.3388-2.5122.29376.4131-0.72646.50230.05810.4316-0.6626-0.3119-0.01930.1358-0.0965-0.1531-0.10990.5104-0.02660.05790.30760.01370.7095-40.950824.1539-9.2877
78.0924-0.78731.06823.90380.22552.2122-0.17350.4343-0.4294-0.04080.1413-0.01980.04660.1074-0.03080.3497-0.03540.01420.2386-0.00350.4116-19.79890.9722.5114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 163 )A28 - 163
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 254 )A164 - 254
3X-RAY DIFFRACTION3chain 'C' and (resid 27 through 66 )C27 - 66
4X-RAY DIFFRACTION4chain 'C' and (resid 67 through 100 )C67 - 100
5X-RAY DIFFRACTION5chain 'C' and (resid 101 through 115 )C101 - 115
6X-RAY DIFFRACTION6chain 'C' and (resid 116 through 163 )C116 - 163
7X-RAY DIFFRACTION7chain 'C' and (resid 164 through 254 )C164 - 254

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