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- PDB-7fi6: Crystal structure of human MICA mutants in complex with natural k... -

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Basic information

Entry
Database: PDB / ID: 7fi6
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 / gamma-delta T cell activation / natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / negative regulation of natural killer cell mediated cytotoxicity ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / gamma-delta T cell activation / natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / T cell mediated cytotoxicity / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / 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 / response to heat / carbohydrate binding / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / external side of plasma membrane / signaling receptor binding / DNA damage response / cell surface / signal transduction / extracellular space / membrane / identical protein binding / 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like ...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 / 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
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: 2.9 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)63,9853
Polymers63,9853
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-15 kcal/mol
Surface area25640 Å2
Unit cell
Length a, b, c (Å)123.600, 123.600, 180.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 93 - 214 / Label seq-ID: 16 - 137

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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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: 31764.508 Da / Num. of mol.: 1 / Mutation: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.4 % / Mosaicity: 0.54 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 2.7 M Sodium chloride, 0.1 M Tris pH 8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9→90.38 Å / Num. obs: 15918 / % possible obs: 100 % / Redundancy: 24 % / CC1/2: 0.995 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.074 / Rrim(I) all: 0.368 / Net I/σ(I): 12 / Num. measured all: 382274 / Scaling rejects: 868
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
2.9-3.0825.32.6536424425380.7550.5392.7072.8100
8.7-90.3820.10.086135966750.9960.020.08824.899.8

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Processing

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

1hyr


Resolution: 2.9→62.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.881 / SU B: 16.784 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 771 4.8 %RANDOM
Rwork0.193 ---
obs0.1963 15138 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.79 Å2 / Biso mean: 53.313 Å2 / Biso min: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2--0.83 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: final / Resolution: 2.9→62.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 0 2 4193
Biso mean---35.17 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173735
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6445841
X-RAY DIFFRACTIONr_angle_other_deg1.211.5758730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6065513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02123.08237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0891523
X-RAY DIFFRACTIONr_chiral_restr0.0610.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
Refine LS restraints NCS

Ens-ID: 1 / Number: 3558 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.9→2.976 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 49 -
Rwork0.263 1108 -
all-1157 -
obs--100 %

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