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- PDB-7tzg: Structure of human LAG3 in complex with antibody single-chain var... -

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Basic information

Entry
Database: PDB / ID: 7tzg
TitleStructure of human LAG3 in complex with antibody single-chain variable fragment
Components
  • Lymphocyte activation gene 3 protein
  • scFvF7
KeywordsIMMUNOSUPPRESSANT / Immune checkpoint / T cell / Complex / Antibody / Ig-like fold
Function / homology
Function and homology information


plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / antigen binding / MHC class II antigen presentation / T cell activation ...plasmacytoid dendritic cell activation / negative regulation of regulatory T cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / MHC class II protein binding / negative regulation of interleukin-2 production / natural killer cell mediated cytotoxicity / regulation of immune response / antigen binding / MHC class II antigen presentation / T cell activation / transmembrane signaling receptor activity / adaptive immune response / cell surface receptor signaling pathway / external side of plasma membrane / innate immune response / cell surface / extracellular region / plasma membrane
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 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 / pdbx_initial_refinement_model
Revision 1.5Oct 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
A: scFvF7
B: scFvF7
C: Lymphocyte activation gene 3 protein
D: Lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,84211
Polymers140,2944
Non-polymers1,5487
Water00
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)78.436, 142.928, 158.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFvF7


Mass: 25802.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Lymphocyte activation gene 3 protein / LAG-3


Mass: 44344.199 Da / Num. of mol.: 2 / Fragment: ectodomain / Mutation: M171I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAG3, FDC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18627
#3: 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.: 7 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1% Tacsimate at pH 5.0, 0.05 M sodium citrate tribasic dihydrate, pH 5.6 and 7% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.71→45.62 Å / Num. obs: 19405 / % possible obs: 99.8 % / Redundancy: 5.092 % / Biso Wilson estimate: 115.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.195 / Rrim(I) all: 0.218 / Χ2: 0.84 / Net I/σ(I): 7.43 / Num. measured all: 98804 / Scaling rejects: 15
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
3.71-3.814.9611.1561.656916140113940.5011.29899.5
3.81-3.915.2620.9772.097298138713870.6191.089100
3.91-4.035.3270.822.567053132413240.7080.912100
4.03-4.155.3430.613.327016131413130.8120.67999.9
4.15-4.295.2510.4784.016648126612660.8670.533100
4.29-4.445.190.374.996301121512140.9240.41399.9
4.44-4.64.8960.3025.725841119411930.9270.3499.9
4.6-4.795.2540.2536.955900112511230.9570.28299.8
4.79-5.015.1020.2327.075546108710870.9610.26100
5.01-5.255.0760.2037.965452107610740.970.22799.8
5.25-5.535.3310.2087.7853209999980.970.23299.9
5.53-5.875.2410.2018.2749849519510.9660.225100
5.87-6.275.0750.2097.945939059050.9680.234100
6.27-6.784.8010.1589.3140098388350.9830.17899.6
6.78-7.425.010.1311.0638887777760.9860.14699.9
7.42-8.34.8310.09514.1633967037030.990.107100
8.3-9.585.0430.06818.7832026366350.9950.07599.8
9.58-11.744.5990.04922.7224975465430.9970.05599.5
11.74-16.64.3820.04722.5519154374370.9980.053100
16.6-45.624.1660.04224.2110292622470.9990.04894.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DSI

6dsi


Resolution: 3.71→45.62 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 971 5 %
Rwork0.2263 18431 -
obs0.2287 19402 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 363.89 Å2 / Biso mean: 148.0848 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.71→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8618 0 98 0 8716
Biso mean--194.06 --
Num. residues----1194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.71-3.910.35471360.315625822718
3.91-4.150.31351360.2625802716
4.15-4.470.27231370.225226002737
4.47-4.920.29681380.201526182756
4.92-5.630.24511370.202126232760
5.63-7.090.29211410.24726602801
7.09-45.620.2441460.209527682914
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)
10.82240.1601-0.54831.52150.28820.30240.85680.6314-1.51770.8401-0.2723-0.81480.2733-0.17720.0760.86090.0962-0.29521.0269-0.31951.5699-21.930110.62040.5721
21.59770.68950.240.9965-0.71190.44750.18490.3624-0.60590.1149-0.00080.35160.2431-0.11520.00010.587-0.0221-0.12090.8144-0.20180.8018-42.286223.0615-10.2315
30.5936-0.78610.59431.8486-1.19010.82470.45670.0677-0.97920.23440.24241.1501-0.9677-0.0690.49760.6694-0.0485-0.30370.8704-0.35610.6201-42.717216.3693-10.9458
4-0.00240.1972-0.08760.14110.18650.19140.16370.5758-1.2470.18320.14630.21720.1935-0.3410.03230.6945-0.092-0.14380.5846-0.13980.6825-47.368822.5702-2.754
50.07020.1540.46012.0279-1.26882.3657-0.3980.4706-0.09990.0715-0.1554-0.5374-0.07590.3757-1.67840.4443-0.05340.09690.9032-0.36940.2649-37.851226.3885-5.4096
61.19780.22830.77930.88161.13670.90940.3373-0.0228-0.2734-0.2412-0.1323-0.0909-0.1910.1424-00.6551-0.0499-0.0230.5906-0.16360.7565-31.587939.60120.269
70.1155-0.09280.51620.87150.00051.01550.1785-0.21540.137-0.2434-0.26710.18760.45760.0585-0.00010.835-0.0409-0.1430.7421-0.19860.91869.90110.2102-33.9015
81.5516-0.05-0.05120.49320.85641.57610.0735-0.0887-2.13490.244-0.3320.06040.01810.3006-0.12150.4769-0.1996-0.16490.4126-0.37290.30487.97754.9281-26.0278
90.33920.50270.82810.89051.01551.01140.03780.26320.47820.1501-0.1448-0.06890.04550.07360.00080.56120.06960.03720.4997-0.09850.478312.9618.824-19.1966
101.2981-0.515-0.61871.1079-0.35650.42680.3448-0.61660.82790.4861-0.1980.2014-0.14130.3957-01.0581-0.2869-0.03311.2925-0.09940.814262.179533.385138.7246
110.896-0.3244-0.61950.3428-0.12520.43270.61451.30510.44540.0964-0.3777-0.68370.03020.03750.02020.90360.03740.11630.73120.27440.918240.88620.490226.5178
120.67491.12870.67830.3874-0.42891.21380.17050.1466-0.1317-0.06350.0412-0.14370.40150.57490.00031.00630.1035-0.06480.8242-0.01080.911229.768-9.91191.5752
130.4487-0.39670.39790.71640.09710.21510.55480.0747-0.61830.94460.0731-2.3935-0.6138-0.06330.03741.685-0.3668-0.42931.52-0.27441.649825.966848.407861.8517
140.7256-0.19640.65892.0124-0.22120.6543-0.8252-0.1331-0.01660.8304-0.01930.94020.0063-0.0864-0.58551.6312-0.31650.40610.7938-0.11721.508915.902856.950756.7004
152.1016-0.688-1.41751.3574-0.20511.305-0.1091-0.1099-0.4087-0.013-0.00420.6941-0.1096-0.2016-0.00020.9728-0.0145-0.09550.93710.21710.940921.547533.254944.8655
160.0379-0.47570.10472.266-0.76980.0178-0.00090.3770.7366-0.075-0.25440.77920.35740.57350.0020.80850.2493-0.2911.1276-0.01941.12894.64989.568220.269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 356 through 427 )D356 - 427
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 63 )A3 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 85 )A64 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 100 )A86 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 142 )A101 - 142
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 247 )A143 - 247
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 85 )B3 - 85
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 148 )B86 - 148
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 248 )B149 - 248
10X-RAY DIFFRACTION10chain 'C' and (resid 30 through 184 )C30 - 184
11X-RAY DIFFRACTION11chain 'C' and (resid 185 through 257 )C185 - 257
12X-RAY DIFFRACTION12chain 'C' and (resid 258 through 430 )C258 - 430
13X-RAY DIFFRACTION13chain 'D' and (resid 25 through 60 )D25 - 60
14X-RAY DIFFRACTION14chain 'D' and (resid 61 through 123 )D61 - 123
15X-RAY DIFFRACTION15chain 'D' and (resid 124 through 244 )D124 - 244
16X-RAY DIFFRACTION16chain 'D' and (resid 245 through 355 )D245 - 355

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