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- PDB-8ea6: NKG2D complexed with inhibitor 3e -

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Basic information

Entry
Database: PDB / ID: 8ea6
TitleNKG2D complexed with inhibitor 3e
ComponentsNKG2-D type II integral membrane protein
KeywordsIMMUNOSUPPRESSANT/INHIBITOR / NKG2D / Immune System / IMMUNOSUPPRESSANT / IMMUNOSUPPRESSANT-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / DAP12 signaling / signaling receptor activity / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Chem-VMB / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsThompson, A.A. / Grant, J.C. / Karpowich, N.K. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Identification of small-molecule protein-protein interaction inhibitors for NKG2D.
Authors: Thompson, A.A. / Harbut, M.B. / Kung, P.P. / Karpowich, N.K. / Branson, J.D. / Grant, J.C. / Hagan, D. / Pascual, H.A. / Bai, G. / Zavareh, R.B. / Coate, H.R. / Collins, B.C. / Cote, M. / ...Authors: Thompson, A.A. / Harbut, M.B. / Kung, P.P. / Karpowich, N.K. / Branson, J.D. / Grant, J.C. / Hagan, D. / Pascual, H.A. / Bai, G. / Zavareh, R.B. / Coate, H.R. / Collins, B.C. / Cote, M. / Gelin, C.F. / Damm-Ganamet, K.L. / Gholami, H. / Huff, A.R. / Limon, L. / Lumb, K.J. / Mak, P.A. / Nakafuku, K.M. / Price, E.V. / Shih, A.Y. / Tootoonchi, M. / Vellore, N.A. / Wang, J. / Wei, N. / Ziff, J. / Berger, S.B. / Edwards, J.P. / Gardet, A. / Sun, S. / Towne, J.E. / Venable, J.D. / Shi, Z. / Venkatesan, H. / Rives, M.L. / Sharma, S. / Shireman, B.T. / Allen, S.J.
History
DepositionAug 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
B: NKG2-D type II integral membrane protein
A: NKG2-D type II integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2563
Polymers29,7622
Non-polymers4941
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-13 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.635, 44.675, 64.953
Angle α, β, γ (deg.)90.000, 106.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-492-

HOH

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Components

#1: Protein NKG2-D type II integral membrane protein / Killer cell lectin-like receptor subfamily K member 1 / NK cell receptor D / NKG2-D-activating NK receptor


Mass: 14880.832 Da / Num. of mol.: 2 / Mutation: S117E,I173S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Production host: Escherichia coli (E. coli) / References: UniProt: P26718
#2: Chemical ChemComp-VMB / N-{(1S)-2-(dimethylamino)-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4'-(trifluoromethyl)[1,1'-biphenyl]-2-carboxamide


Mass: 494.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H20F6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 - 0.22 M NaNO3, 20- 31 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→40.55 Å / Num. obs: 29231 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.687 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Net I/σ(I): 7.2 / Num. measured all: 98015
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.73-1.763.41471613890.7741.44496.9
4.69-40.563.620.4551915380.0250.04799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MPU

1mpu


Resolution: 1.73→33.9 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1440 4.93 %
Rwork0.1862 27755 -
obs0.1876 29195 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.56 Å2 / Biso mean: 33.8048 Å2 / Biso min: 13.59 Å2
Refinement stepCycle: final / Resolution: 1.73→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 35 215 2206
Biso mean--21.47 41.26 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.790.38261370.33722718285598
1.79-1.860.33171310.282927482879100
1.86-1.950.29571610.238127512912100
1.95-2.050.24391480.220127492897100
2.05-2.180.22221380.202627512889100
2.18-2.340.22851390.197527812920100
2.34-2.580.25781430.188327822925100
2.58-2.950.22191500.188227952945100
2.95-3.720.20341380.164928162954100
3.72-33.90.15941550.15428643019100
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)
14.52572.01263.50816.3742-1.26788.843-0.187-0.36350.5768-0.0684-0.168-0.1677-0.7390.42670.51920.38680.0298-0.01770.34430.03720.28180.264-8.078.262
25.29672.1647-3.39823.5944-2.7234.8490.18060.02480.17220.0505-0.04780.2756-0.2330.0344-0.14070.20830.0033-0.03020.27560.01070.2006-7.028-18.62317.573
35.03070.2436-0.95612.3827-0.31774.7663-0.12840.4339-0.4176-0.20810.02630.02170.2866-0.08510.05880.1980.0034-0.00950.2332-0.04930.1963-3.728-28.23912.735
46.41450.45730.43144.8768-1.71435.3891-0.0050.4309-0.4225-0.3732-0.07950.12810.54180.2650.1910.36780.0097-0.02070.368-0.12370.3215-5.165-35.35812.736
54.3340.2235-1.46244.164-0.46093.6733-0.07630.1002-0.2503-0.141-0.0213-0.03880.18980.13560.03790.1215-0.0035-0.01580.2514-0.01520.144-4.412-27.33917.722
63.7466-0.21124.99712.811-1.66117.3311-0.40630.70040.0798-0.2489-0.1137-0.2497-0.28050.27890.46720.4-0.00550.02050.47290.0450.28376.705-8.4216.07
77.24781.46060.93640.87260.28882.8244-0.30651.0406-0.2939-0.19230.2614-0.221-0.11870.20640.06060.2564-0.08430.03110.318-0.02930.213218.142-11.74313.989
86.49550.4973-0.73033.36081.27083.2901-0.16530.46650.3597-0.03440.11280.1302-0.3192-0.13840.00390.1839-0.0224-0.03660.15090.03730.160212.376-8.40521.573
95.1251-0.40466.76060.3741-0.46398.9615-0.385-0.18280.58440.23950.1246-0.6325-0.2680.17410.29170.3785-0.0306-0.0980.2907-0.02190.396726.537-0.30327.896
104.62670.1434-0.58382.7418-0.52442.3305-0.0278-0.1403-0.00850.16170.01540.0054-0.37580.1729-0.0130.2607-0.042-0.04880.136-0.04020.223620.321-4.14429.436
115.62380.7725-0.92441.8541.33233.9954-0.04390.2868-0.0762-0.00450.0767-0.1308-0.19870.0994-0.00390.1912-0.04080.00160.09170.01290.228619.439-11.53323.706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 94:103 )A94 - 103
2X-RAY DIFFRACTION2( CHAIN A AND RESID 104:130 )A104 - 130
3X-RAY DIFFRACTION3( CHAIN A AND RESID 131:168 )A131 - 168
4X-RAY DIFFRACTION4( CHAIN A AND RESID 169:188 )A169 - 188
5X-RAY DIFFRACTION5( CHAIN A AND ( RESID 189:214 OR RESID 323:350 ) )A189 - 214
6X-RAY DIFFRACTION5( CHAIN A AND ( RESID 189:214 OR RESID 323:350 ) )A323 - 350
7X-RAY DIFFRACTION6( CHAIN B AND RESID 94:103 )B94 - 103
8X-RAY DIFFRACTION7( CHAIN B AND RESID 104:130 )B104 - 130
9X-RAY DIFFRACTION8( CHAIN B AND RESID 131:156 )B131 - 156
10X-RAY DIFFRACTION9( CHAIN B AND RESID 157:168 )B157 - 168
11X-RAY DIFFRACTION10( CHAIN B AND RESID 169:188 )B169 - 188
12X-RAY DIFFRACTION11( CHAIN B AND RESID 189:214 )B189 - 214

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