[English] 日本語
Yorodumi
- PDB-8ea5: NKG2D complexed with inhibitor 1a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ea5
TitleNKG2D complexed with inhibitor 1a
ComponentsNKG2-D type II integral membrane protein
KeywordsIMMUNOSUPPRESSANT/INHIBITOR / NKG2D / Immune System / IMMUNOSUPPRESSANT-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / 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 / 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
TRIETHYLENE GLYCOL / Chem-VN8 / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,5085
Polymers29,7622
Non-polymers7473
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-8 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.107, 43.671, 77.766
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-451-

HOH

-
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-VN8 / (3S,5aS,8aR)-3-benzyl-6-[(3,5-dichlorophenyl)methyl]-1,4-dimethyloctahydropyrrolo[3,2-e][1,4]diazepine-2,5-dione


Mass: 446.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25Cl2N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 - 0.22 M NaNO3 20- 31 % (w/v) PEG 3350

-
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: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→40.13 Å / Num. obs: 33491 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.414 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 7 / Num. measured all: 112256
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.63-1.663.41.9556916190.4380.82895.4
4.42-40.143.613.3635217780.0210.04100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 2

-
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: 1.63→40.13 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1676 5.01 %
Rwork0.1887 --
obs0.1898 33467 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 50 126 2099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132025
X-RAY DIFFRACTIONf_angle_d1.5152737
X-RAY DIFFRACTIONf_dihedral_angle_d7.68263
X-RAY DIFFRACTIONf_chiral_restr0.081275
X-RAY DIFFRACTIONf_plane_restr0.009346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.26571300.24682563X-RAY DIFFRACTION96
1.68-1.730.28341400.23032617X-RAY DIFFRACTION98
1.73-1.790.25621320.22572619X-RAY DIFFRACTION98
1.79-1.870.2171320.20242624X-RAY DIFFRACTION98
1.87-1.950.22481450.20132617X-RAY DIFFRACTION98
1.95-2.050.20541590.1892631X-RAY DIFFRACTION99
2.05-2.180.24321370.1822645X-RAY DIFFRACTION99
2.18-2.350.20831220.18832657X-RAY DIFFRACTION99
2.35-2.590.21291270.1822667X-RAY DIFFRACTION99
2.59-2.960.22921450.19552696X-RAY DIFFRACTION100
2.96-3.730.20671450.1852704X-RAY DIFFRACTION100
3.73-40.130.1791620.17582751X-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)
13.74713.4970.51443.35311.48418.6160.02950.29160.0669-0.51040.12330.0124-0.2306-0.1014-0.25990.2344-0.01750.02490.14850.01830.1313.1991-4.35667.1697
26.0139-1.22761.56572.6697-0.55064.66570.09510.0909-0.2444-0.08430.0632-0.24740.1150.3122-0.11350.1316-0.01870.01030.1569-0.02320.143312.5943-8.948419.7321
36.3176-1.63780.67664.31750.33385.4344-0.0326-0.0930.33720.16080.02370.1039-0.4303-0.1862-0.03820.2274-0.01040.00860.13220.01160.1194.9973-0.494721.9672
45.5035-1.10090.60513.6704-0.41695.06960.1125-0.2132-0.07170.6104-0.0411-0.0196-0.2008-0.0116-0.08630.2339-0.0178-0.00110.1443-0.01550.08427.5568-5.705328.5623
54.4923-0.1959-0.9832.56581.48842.73550.0778-0.13410.62670.26190.094-0.0375-0.4985-0.0138-0.13880.4037-0.00880.00340.1766-0.02290.18776.81592.481231.4235
62.01151.3258-3.67410.32970.25844.6413-0.1385-0.9969-0.35280.73770.2135-0.15930.24260.6172-0.10890.562-0.0289-0.07130.5103-0.02930.335113.4606-7.381341.4495
74.9279-0.5053-0.68713.11621.27653.6769-0.0219-0.2501-0.15040.3950.0397-0.2008-0.07080.2288-0.03580.1808-0.0263-0.02580.1204-0.00030.14349.9274-8.03828.2352
86.27693.3203-2.20397.3072-2.45158.9331-0.1021-0.2564-0.0596-0.4376-0.0028-0.0004-0.31570.20620.08630.24630.05080.01820.15950.02180.2659-1.8166-5.37127.3522
95.87043.8806-3.06025.2169-3.88673.83520.1815-0.13320.49650.1712-0.01720.3937-0.2635-0.2549-0.19470.12860.01110.00780.1737-0.04880.266-10.7047-16.957315.3927
106.1506-0.3431-2.04044.6704-0.50345.06560.1159-0.0793-0.03-0.21640.0422-0.12570.22850.0492-0.13850.1311-0.0024-0.03410.0959-0.02910.1632-4.6415-24.037311.5191
119.3938-1.27392.28555.8673-0.59285.69980.04930.3958-0.6753-0.4302-0.11690.13220.45070.15680.02010.2931-0.0169-0.05480.1333-0.10470.2439-5.8846-33.27911.1358
125.6099-0.2157-1.12795.7507-0.62583.11370.099-0.0817-0.0109-0.06340.02560.07550.18770.0389-0.1250.1051-0.0172-0.02350.1403-0.03510.1043-7.3601-24.960915.8627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 168 )
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 188 )
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 215 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 103 )
9X-RAY DIFFRACTION9chain 'B' and (resid 104 through 130 )
10X-RAY DIFFRACTION10chain 'B' and (resid 131 through 169 )
11X-RAY DIFFRACTION11chain 'B' and (resid 170 through 188 )
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 216 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more