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- PDB-7fi9: Crystal structure of human MICA mutants in complex with natural k... -

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Basic information

Entry
Database: PDB / ID: 7fi9
TitleCrystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D
Components
  • MHC class I polypeptide-related sequence A
  • NKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM / NKG2D / MICA / thermal stability
Function / homology
Function and homology information


immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / gamma-delta T cell activation / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell activation ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / gamma-delta T cell activation / negative 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 / T cell mediated cytotoxicity / 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 / response to heat / carbohydrate binding / defense response to virus / killing of cells of another organism / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / receptor ligand activity / external side of plasma membrane / DNA damage response / cell surface / signal transduction / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NKG2-D type II integral membrane protein / MHC class I polypeptide-related sequence A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsCai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J.
CitationJournal: to be published
Title: Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D
Authors: Cai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J.
History
DepositionJul 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 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

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
C: MHC class I polypeptide-related sequence A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2905
Polymers64,1063
Non-polymers1842
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-13 kcal/mol
Surface area25850 Å2
Unit cell
Length a, b, c (Å)123.808, 123.808, 181.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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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: 16110.215 Da / Num. of mol.: 2
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: Protein MHC class I polypeptide-related sequence A / MIC-A


Mass: 31885.621 Da / Num. of mol.: 1
Mutation: N8D, L9F, L34I, Q108H, Q120W, W127F, L146W, Y157F, H161R V177I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICA, PERB11.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q29983
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.71 Å3/Da / Density % sol: 54.61 % / Mosaicity: 0.18 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.7 M Ammonium tartrate dibasic, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.16→19.71 Å / Num. obs: 37683 / % possible obs: 99.2 % / Redundancy: 25.1 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.014 / Rrim(I) all: 0.072 / Net I/σ(I): 32.4 / Num. measured all: 944381 / Scaling rejects: 55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.16-2.2315.61.5314667529830.6330.3811.5821.992.4
8.91-19.7120.90.024117035590.9990.0050.025106.490.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hyr

1hyr


Resolution: 2.16→19.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.242 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1891 5 %RANDOM
Rwork0.1876 ---
obs0.19 35750 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.24 Å2 / Biso mean: 51.159 Å2 / Biso min: 29.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0 Å2
2---0.94 Å20 Å2
3---1.88 Å2
Refinement stepCycle: final / Resolution: 2.16→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 12 148 4386
Biso mean--82.35 50.52 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134373
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173780
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6425933
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5748829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8325520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00222.946241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72415744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02942
LS refinement shellResolution: 2.161→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 111 -
Rwork0.29 2371 -
all-2482 -
obs--90.75 %

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