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- PDB-8ea9: NKG2D complexed with inhibitor 4d -

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Basic information

Entry
Database: PDB / ID: 8ea9
TitleNKG2D complexed with inhibitor 4d
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 / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / positive regulation of 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 / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / positive regulation of 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 nitric oxide biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / membrane / identical protein binding / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-VMQ / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 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

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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)30,8827
Polymers29,7622
Non-polymers1,1205
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-3 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.719, 43.400, 64.777
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-459-

HOH

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Components

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Protein , 1 types, 2 molecules BA

#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

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-VMQ / N-[(1S)-1-[3,5-bis(trifluoromethyl)phenyl]-2-(dimethylamino)-2-oxoethyl]-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide


Mass: 563.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18F9N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.43 %
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: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→43.47 Å / Num. obs: 36337 / % possible obs: 97.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.15 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 13.3 / Num. measured all: 114849
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.58-1.6123.8280514260.1230.19176
4.29-43.493.424.1663519430.0210.03999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MPU

1mpu


Resolution: 1.58→32.28 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 1760 4.85 %
Rwork0.1795 --
obs0.181 36315 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 76 154 2182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052098
X-RAY DIFFRACTIONf_angle_d0.8722836
X-RAY DIFFRACTIONf_dihedral_angle_d8.83285
X-RAY DIFFRACTIONf_chiral_restr0.089280
X-RAY DIFFRACTIONf_plane_restr0.004361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.21471060.19312125X-RAY DIFFRACTION79
1.62-1.670.19161500.18492440X-RAY DIFFRACTION90
1.67-1.720.2361370.18682631X-RAY DIFFRACTION98
1.72-1.790.25721370.18462727X-RAY DIFFRACTION100
1.79-1.860.20821210.1842725X-RAY DIFFRACTION100
1.86-1.940.18721330.17532719X-RAY DIFFRACTION100
1.94-2.040.2221340.16932727X-RAY DIFFRACTION100
2.04-2.170.21961460.17662737X-RAY DIFFRACTION100
2.17-2.340.20931290.18152676X-RAY DIFFRACTION100
2.34-2.580.21211410.182743X-RAY DIFFRACTION100
2.58-2.950.2171400.18562726X-RAY DIFFRACTION100
2.95-3.710.19721550.18742749X-RAY DIFFRACTION100
3.71-32.280.21821310.17082830X-RAY DIFFRACTION100
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)
12.55940.91850.52743.1528-0.52331.62080.01730.03620.0531-0.06020.00710.1401-0.0922-0.1113-0.00420.15040.009-0.00430.1467-0.02270.1184-0.289-18.323113.534
22.6594-0.3855-0.00872.6150.31643.6783-0.07590.1495-0.4161-0.2641-0.20760.46170.4457-0.32350.120.2564-0.0403-0.03760.2028-0.04970.3328-4.7536-32.69598.395
31.8378-0.1045-0.32842.86851.02381.59360.0806-0.0448-0.28360.0013-0.0288-0.00370.181-0.0829-0.0410.1949-0.0178-0.03130.18810.00460.2403-1.0144-30.080517.8085
42.68290.49731.50561.06910.24741.99690.00170.3591-0.2088-0.17680.07090.0152-0.09310.2739-0.08380.2104-0.01330.01090.2086-0.01170.15915.9629-8.993512.6026
53.3848-0.6922-0.22961.84670.20462.599-0.1124-0.07130.06510.12430.05450.001-0.25750.010.06060.2059-0.0102-0.00640.1628-0.00410.156915.8155-5.1523.1129
62.83950.27910.40341.26580.89532.2977-0.1164-0.04680.04920.01440.075-0.077-0.24240.15330.03520.1695-0.0224-0.01940.14160.00390.171820.1246-5.782726.0715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 91 through 154 )
2X-RAY DIFFRACTION2chain 'B' and (resid 155 through 178 )
3X-RAY DIFFRACTION3chain 'B' and (resid 179 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 215 )

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