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- PDB-7tzh: Structure of human LAG3 domains 3-4 in complex with antibody sing... -

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Basic information

Entry
Database: PDB / ID: 7tzh
TitleStructure of human LAG3 domains 3-4 in complex with antibody single chain-variable fragment
Components
  • Lymphocyte activation gene 3 protein
  • scFvF7
KeywordsIMMUNOSUPPRESSANT / Immune checkpoint / cell surface / 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: 2.43 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 1.5Nov 13, 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
C: scFvF7
D: Lymphocyte activation gene 3 protein
A: scFvF7
B: Lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0216
Polymers91,5784
Non-polymers4422
Water3,045169
1
C: scFvF7
D: Lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0103
Polymers45,7892
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: scFvF7
B: Lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0103
Polymers45,7892
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.155, 78.521, 107.166
Angle α, β, γ (deg.)90.000, 111.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

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Components

#1: Antibody scFvF7


Mass: 25731.559 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: 20057.531 Da / Num. of mol.: 2 / Fragment: ectodomain
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.: 2 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.1, 13% PEG20000

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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: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.43→46.48 Å / Num. obs: 34666 / % possible obs: 99.55 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.39 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 11.35
Reflection shellResolution: 2.43→2.52 Å / Num. unique obs: 3383 / CC1/2: 0.707 / CC star: 0.91 / % possible all: 98.25

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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: 2.43→46.48 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1724 4.98 %
Rwork0.2124 32911 -
obs0.2146 34635 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.54 Å2 / Biso mean: 73.2572 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 2.43→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 28 169 6101
Biso mean--120.69 55.54 -
Num. residues----803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.50.3541410.3222695283698
2.5-2.580.35551440.2992682282699
2.58-2.680.31491390.277627422881100
2.68-2.780.31691420.27627312873100
2.78-2.910.3171230.268827622885100
2.91-3.060.27441520.255727422894100
3.06-3.250.25641420.230627442886100
3.26-3.510.31291530.223627192872100
3.51-3.860.28951620.212827322894100
3.86-4.420.22741390.181727732912100
4.42-5.560.19851550.162227562911100
5.56-46.480.2011320.19242833296599
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)
10.3105-0.0906-0.55430.87530.04511.22120.4086-0.25870.1955-0.4014-0.36150.737-0.6376-0.0628-0.05631.2183-0.2164-0.29681.0930.03040.742813.9197-45.4537.2798
20.20490.24830.11160.39480.09710.2649-0.08-0.12350.0614-0.088-0.09780.0723-0.16910.3393-0.32991.2852-0.94240.26651.41390.04580.762329.728-46.91638.4581
30.3057-0.0392-0.04312.2516-0.08132.2085-0.30520.3380.2067-0.38760.07750.2324-0.94070.4104-0.1150.7973-0.36870.0320.99940.0240.372321.9377-56.719939.7562
42.2853-0.0378-0.2980.9678-0.26822.28250.22050.001-0.0072-0.3709-0.2711-0.3553-0.96820.5257-0.02991.0547-0.4167-0.04131.11950.00980.607422.7194-52.096732.7332
52.35450.28140.01872.21810.60291.08530.0012-0.19860.0988-0.3474-0.19850.7767-0.64780.1293-0.11961.0943-0.2415-0.14880.9640.11470.536215.4416-53.050339.9157
62.07991.07610.673.54050.95180.3947-0.0457-0.14190.5290.1836-0.2998-0.1628-0.26050.3878-0.99990.5381-0.9775-0.00961.6626-0.25820.524129.9845-55.502746.7701
70.5364-0.6236-0.09931.3058-0.49910.6757-0.1193-0.09-0.1171-0.178-0.13920.4672-0.4723-0.179-0.01741.0156-0.1369-0.02570.891-0.16250.517513.0956-58.487941.3251
80.27780.2161-0.37770.2955-0.55581.15670.0871-0.488-0.34710.23480.13310.00840.299-0.045-0.01440.5226-0.14670.0660.8377-0.04550.49417.3773-63.91465.2643
91.08140.0672-0.54741.70311.01352.5091-0.16460.2505-0.1431-0.12680.2096-0.2713-0.21880.85250.03360.4617-0.08720.05211.0417-0.07540.37525.4011-66.754754.7657
101.5222-0.1369-0.12960.91030.31642.1128-0.0355-0.03490.33870.08270.09950.1254-0.27230.87690.00310.5237-0.19030.02571.1637-0.13350.412528.3268-60.365259.2393
111.3863-0.1228-0.73491.28760.08752.3971-0.20350.11070.517-0.03570.33470.2047-0.4930.4473-0.05890.5192-0.25910.00840.9018-0.0430.409420.8982-60.027957.6351
123.7206-1.48481.0151.8021.13722.28650.0789-0.0623-0.0070.369-0.0854-0.24150.360.07130.18020.8374-0.00920.01020.83080.12190.609936.6019-92.465233.5817
134.9553-3.4349-6.11953.21643.90937.685-0.5001-1.2788-0.64731.50170.4352-0.47551.27590.83990.10711.42770.2498-0.24851.3648-0.00141.284150.4721-106.982237.3375
141.299-0.4835-0.34351.29770.48480.87680.32420.2088-0.77040.1534-0.1116-0.01180.46410.09220.19810.88880.0836-0.15470.9561-0.0440.955938.0124-101.566929.5198
153.89010.13730.20062.69180.73284.6435-0.24380.1006-0.0408-0.4576-0.04250.43370.0195-0.33650.01520.6123-0.10030.01690.909-0.02420.402125.3102-75.040625.3716
162.256-0.7171-0.49112.20470.48593.14760.1046-0.74530.10540.0188-0.1540.30390.01860.48760.07720.5739-0.12110.06591.0533-0.09180.381330.0772-75.762736.5273
173.16520.1719-0.47641.54530.32162.31610.0057-0.3850.29730.3864-0.16170.3853-0.2339-0.07770.01180.7185-0.07730.11880.9792-0.05290.525931.0979-72.69931.7526
181.42160.5554-1.35353.4735-4.30918.29420.0185-0.217-0.41080.1627-0.6633-0.4003-0.07770.56370.36250.57220.05220.01991.01170.08920.534337.9242-77.215628.5667
192.29560.42310.32221.447-0.1131.7935-0.0126-0.0443-0.1188-0.0511-0.02410.37290.2623-0.62490.04890.251-0.09-0.02240.4349-0.01350.411733.6933-71.6094-1.3047
201.3690.1646-0.08041.06150.02962.1472-0.0490.2696-0.0172-0.15840.03250.0465-0.0406-0.02150.04430.2059-0.036-0.0250.2843-0.02190.298150.2847-65.2097-12.8045
212.42410.45091.26161.9411.17251.27970.0511-0.20440.2176-0.2705-0.0694-0.3924-0.67410.51510.00230.6658-0.1188-0.06460.7903-0.10020.932457.6016-36.737116.7923
221.5771-0.5757-0.75120.22310.30960.4696-0.1323-0.58410.03410.4631-0.0218-0.4637-0.20650.9585-0.18270.8708-0.1912-0.21191.3368-0.22971.457571.3563-30.333425.2917
231.21221.86871.1613.13742.68914.3093-0.1152-0.40670.71360.02560.08470.068-1.028-0.42870.02751.17840.0027-0.32580.6101-0.20861.173355.452-23.348322.0276
244.35321.33320.96161.22830.33921.6711-0.1435-0.82410.41890.0771-0.3203-0.3208-0.20370.1356-0.06470.7240.0452-0.24240.9123-0.23760.961356.8621-32.80225.2746
250.8478-0.23130.26070.0704-0.13420.5463-0.01-0.07150.4440.0030.1951-0.4054-0.93930.9497-0.20821.6543-0.5619-0.67810.6738-0.27841.380564.0512-22.932319.592
260.7504-0.57531.67781.0317-0.68964.3494-0.47380.29870.9302-0.1176-0.62070.0293-1.16540.5147-0.57960.35710.0968-0.15250.6513-0.20490.83150.0691-36.02315.5483
270.41010.42341.15510.47541.2123.24990.8927-0.91961.52220.6333-0.89453.00380.6957-1.78280.26820.5611-0.1828-0.03381.219-0.34791.674332.1498-50.509413.9092
281.6912-0.2674-0.10911.84441.42721.49040.0977-0.04360.1102-0.1333-0.2580.0789-0.08-0.17350.05880.3974-0.0049-0.13610.4916-0.06010.446346.4924-51.93428.598
290.45660.7408-0.2061.4055-0.3910.10370.0956-0.46060.17140.44-0.12390.66510.8581-0.6173-0.12470.6308-0.2258-0.04380.7927-0.01890.599834.7422-56.662913.9332
304.49851.4261-0.66316.8629-2.23945.4639-0.2024-0.1939-0.10540.0026-0.02380.04540.520.01310.16390.59250.0006-0.04880.4903-0.00240.359948.2428-52.24911.4132
311.4624-0.13620.28840.9880.63990.80110.0481-0.8941-0.41810.7906-0.4896-0.20430.7679-0.38730.22380.6016-0.21060.01010.8976-0.03130.459546.206-53.414920.4872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 4 through 19 )C4 - 19
2X-RAY DIFFRACTION2chain 'C' and (resid 20 through 35 )C20 - 35
3X-RAY DIFFRACTION3chain 'C' and (resid 36 through 62 )C36 - 62
4X-RAY DIFFRACTION4chain 'C' and (resid 63 through 85 )C63 - 85
5X-RAY DIFFRACTION5chain 'C' and (resid 86 through 101 )C86 - 101
6X-RAY DIFFRACTION6chain 'C' and (resid 102 through 117 )C102 - 117
7X-RAY DIFFRACTION7chain 'C' and (resid 118 through 142 )C118 - 142
8X-RAY DIFFRACTION8chain 'C' and (resid 143 through 157 )C143 - 157
9X-RAY DIFFRACTION9chain 'C' and (resid 158 through 177 )C158 - 177
10X-RAY DIFFRACTION10chain 'C' and (resid 178 through 214 )C178 - 214
11X-RAY DIFFRACTION11chain 'C' and (resid 215 through 247 )C215 - 247
12X-RAY DIFFRACTION12chain 'D' and (resid 266 through 280 )D266 - 280
13X-RAY DIFFRACTION13chain 'D' and (resid 281 through 293 )D281 - 293
14X-RAY DIFFRACTION14chain 'D' and (resid 294 through 355 )D294 - 355
15X-RAY DIFFRACTION15chain 'D' and (resid 356 through 371 )D356 - 371
16X-RAY DIFFRACTION16chain 'D' and (resid 372 through 396 )D372 - 396
17X-RAY DIFFRACTION17chain 'D' and (resid 397 through 418 )D397 - 418
18X-RAY DIFFRACTION18chain 'D' and (resid 419 through 434 )D419 - 434
19X-RAY DIFFRACTION19chain 'A' and (resid 1 through 122 )A1 - 122
20X-RAY DIFFRACTION20chain 'A' and (resid 123 through 247 )A123 - 247
21X-RAY DIFFRACTION21chain 'B' and (resid 262 through 280 )B262 - 280
22X-RAY DIFFRACTION22chain 'B' and (resid 281 through 294 )B281 - 294
23X-RAY DIFFRACTION23chain 'B' and (resid 295 through 306 )B295 - 306
24X-RAY DIFFRACTION24chain 'B' and (resid 307 through 328 )B307 - 328
25X-RAY DIFFRACTION25chain 'B' and (resid 329 through 340 )B329 - 340
26X-RAY DIFFRACTION26chain 'B' and (resid 341 through 356 )B341 - 356
27X-RAY DIFFRACTION27chain 'B' and (resid 357 through 371 )B357 - 371
28X-RAY DIFFRACTION28chain 'B' and (resid 372 through 396 )B372 - 396
29X-RAY DIFFRACTION29chain 'B' and (resid 397 through 406 )B397 - 406
30X-RAY DIFFRACTION30chain 'B' and (resid 407 through 418 )B407 - 418
31X-RAY DIFFRACTION31chain 'B' and (resid 419 through 434 )B419 - 434

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