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- PDB-8ea8: NKG2D complexed with inhibitor 4a -

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Basic information

Entry
Database: PDB / ID: 8ea8
TitleNKG2D complexed with inhibitor 4a
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-VML / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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

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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)31,37011
Polymers29,7622
Non-polymers1,6099
Water2,864159
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)100.090, 43.675, 72.591
Angle α, β, γ (deg.)90.000, 125.010, 90.000
Int Tables number5
Space group name H-MC121

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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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-VML / N-{(1S)-2-(dimethylamino)-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide


Mass: 495.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F6N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.66 %
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: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→59.46 Å / Num. obs: 24445 / % possible obs: 96.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.71 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.068 / Net I/σ(I): 12.2 / Num. measured all: 82281
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.77-1.82.94.426199120.1290.23674.8
4.8-59.493.420.1451613320.0240.04599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 2

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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: 1.77→37.25 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1184 4.84 %
Rwork0.1617 23256 -
obs0.1636 24440 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.9 Å2 / Biso mean: 20.4367 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.77→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 109 159 2223
Biso mean--27.03 34 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.850.25461260.16972494262085
1.85-1.950.20451370.15062907304497
1.95-2.070.20521330.1492927306097
2.07-2.230.18011490.14952956310598
2.23-2.450.19651370.15882951308898
2.45-2.810.20771690.16262955312499
2.81-3.540.19931580.17062999315799
3.54-37.250.19441750.165330673242100
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)
13.29090.9168-0.46671.1488-0.15090.1856-0.08760.1707-0.3524-0.1112-0.0556-0.15110.2606-0.20070.09170.22050.01170.0150.1627-0.03040.199919.21287.95966.0043
20.7740.70760.41511.72141.2082.8688-0.0915-0.0026-0.0307-0.0481-0.0342-0.07580.15770.11480.13650.1495-0.00520.01080.13640.00290.10520.21615.735810.5101
31.28560.6927-0.32641.79390.38672.44850.0172-0.3007-0.29390.2208-0.3178-0.46990.24260.3258-0.00510.1131-0.0292-0.03930.27330.07870.234431.994223.1619.025
41.60150.3422-0.14050.9743-0.42852.48130.07070.03050.0996-0.1063-0.0558-0.0242-0.23450.041-0.01790.13440.00710.01450.0937-0.00240.11922.482329.2218.8146
53.5914-0.78111.01570.8920.36472.30480.1642-0.68390.25260.15640.00290.021-0.4386-0.0421-0.07590.2704-0.03230.07790.1858-0.05550.227522.684239.68917.7628
61.55850.22550.33222.1112-0.29221.03020.0835-0.1070.0650.0339-0.1325-0.0987-0.08180.12020.04930.1116-0.0267-0.00040.13830.00170.132923.273129.033316.8708
70.632-0.1754-0.90530.90550.33731.3058-0.07880.1779-0.0052-0.1762-0.0144-0.17180.20850.01590.03810.1620.00020.02030.1216-0.00790.120413.50578.53388.7734
82.0359-0.5597-1.04141.38761.21551.99710.0820.39690.2669-0.34610.03090.0412-0.0886-0.21640.00020.1236-0.0244-0.05230.22060.04060.1389-4.584311.193313.8473
92.1472-0.66540.15331.9438-0.06141.37210.002-0.0891-0.13720.06440.01770.00690.1947-0.036-0.02720.111-0.0176-0.00310.08210.00730.07125.42745.099221.6364
101.0526-0.0154-0.09841.21110.15050.964-0.1004-0.0981-0.0911-0.03860.08520.05170.1443-0.0657-0.01970.1513-0.0307-0.00890.11680.02820.13421.7332.587228.1023
111.2445-0.0057-0.1370.767-0.52491.21790.0164-0.0051-0.01560.01060.03090.04220.0786-0.1033-0.020.089-0.0146-0.01630.1061-0.00550.10061.858910.091522.751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 91 through 103 )B91 - 103
2X-RAY DIFFRACTION2chain 'B' and (resid 104 through 114 )B104 - 114
3X-RAY DIFFRACTION3chain 'B' and (resid 115 through 130 )B115 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 131 through 179 )B131 - 179
5X-RAY DIFFRACTION5chain 'B' and (resid 180 through 188 )B180 - 188
6X-RAY DIFFRACTION6chain 'B' and (resid 189 through 214 )B189 - 214
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 114 )A93 - 114
8X-RAY DIFFRACTION8chain 'A' and (resid 115 through 130 )A115 - 130
9X-RAY DIFFRACTION9chain 'A' and (resid 131 through 168 )A131 - 168
10X-RAY DIFFRACTION10chain 'A' and (resid 169 through 188 )A169 - 188
11X-RAY DIFFRACTION11chain 'A' and (resid 189 through 214 )A189 - 214

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