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- PDB-4n8v: Crystal structure of killer cell immunoglobulin-like receptor KIR... -

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Basic information

Entry
Database: PDB / ID: 4n8v
TitleCrystal structure of killer cell immunoglobulin-like receptor KIR2DS2 in complex with HLA-A
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-11 alpha chain
  • Killer cell immunoglobulin-like receptor 2DS2
  • peptide from Virion membrane protein A14
KeywordsIMMUNE SYSTEM / Antigen presentation / Cell lysing / Kir binding / Membrane / KIR2DS2 / Activating KIR
Function / homology
Function and homology information


stimulatory killer cell immunoglobulin-like receptor signaling pathway / immune response-regulating signaling pathway / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...stimulatory killer cell immunoglobulin-like receptor signaling pathway / immune response-regulating signaling pathway / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / transmembrane signaling receptor activity / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / viral envelope / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum
Similarity search - Function
Poxvirus A14, virion envelope / Poxvirus virion envelope protein A14 / : / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...Poxvirus A14, virion envelope / Poxvirus virion envelope protein A14 / : / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Killer cell immunoglobulin-like receptor 2DS2 / Beta-2-microglobulin / Virion membrane protein OPG140
Similarity search - Component
Biological speciesHomo sapiens (human)
Vaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, J.X. / Ren, E.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Activating killer cell immunoglobulin-like receptor 2DS2 binds to HLA-A*11
Authors: Liu, J.X. / Xiao, Z.W. / Ko, H.L. / Shen, M.X. / Ren, E.C.
History
DepositionOct 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Killer cell immunoglobulin-like receptor 2DS2
I: Killer cell immunoglobulin-like receptor 2DS2
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: peptide from Virion membrane protein A14
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: peptide from Virion membrane protein A14


Theoretical massNumber of molelcules
Total (without water)133,8298
Polymers133,8298
Non-polymers00
Water2,234124
1
G: Killer cell immunoglobulin-like receptor 2DS2
A: HLA class I histocompatibility antigen, A-11 alpha chain
B: Beta-2-microglobulin
C: peptide from Virion membrane protein A14


Theoretical massNumber of molelcules
Total (without water)66,9154
Polymers66,9154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Killer cell immunoglobulin-like receptor 2DS2
D: HLA class I histocompatibility antigen, A-11 alpha chain
E: Beta-2-microglobulin
F: peptide from Virion membrane protein A14


Theoretical massNumber of molelcules
Total (without water)66,9154
Polymers66,9154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.550, 94.670, 228.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21I
12A
22D
13B
23E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTHRTHRGA7 - 2008 - 201
21LYSLYSTHRTHRIB7 - 2008 - 201
12GLYGLYTRPTRPAC1 - 2741 - 274
22GLYGLYTRPTRPDF1 - 2741 - 274
13ILEILEASPASPBD1 - 982 - 99
23ILEILEASPASPEG1 - 982 - 99

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Killer cell immunoglobulin-like receptor 2DS2 / KIR2DS2


Mass: 22179.795 Da / Num. of mol.: 2 / Fragment: UNP residues 22-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DS2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P43631
#2: Protein HLA class I histocompatibility antigen, A-11 alpha chain / HLA-A*11:01 / MHC class I antigen A*11


Mass: 31725.936 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P13746, UniProt: P04439*PLUS
#3: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein/peptide peptide from Virion membrane protein A14


Mass: 1129.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IEDB id 41975 / Source: (synth.) Vaccinia virus WR / References: UniProt: Q76ZQ3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG 3350, 2% TACSIMATE, 0.1M TRI-SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.5→72.89 Å / Num. all: 50112 / Num. obs: 52897 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.5-2.637.40.5842.476180.58499.5
2.63-2.797.70.3963.672820.39699.4
2.79-2.997.60.2794.968050.27999.3
2.99-3.237.60.2056.963330.20599.2
3.23-3.537.60.1699.158810.16999

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q94, 1IM9

1q94

1im9


Resolution: 2.5→66.53 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.098 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.488 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25699 2684 5.1 %RANDOM
Rwork0.22221 ---
obs0.22398 50112 99.31 %-
all-52897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.721 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→66.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 0 124 9364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199508
X-RAY DIFFRACTIONr_bond_other_d0.0030.028583
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.94112908
X-RAY DIFFRACTIONr_angle_other_deg0.8793.00219769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33251135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2523.223484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.123151533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9091578
X-RAY DIFFRACTIONr_chiral_restr0.0760.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110831
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022319
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G104490.05
12I104490.05
21A148920.11
22D148920.11
31B55200.1
32E55200.1
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 185 -
Rwork0.249 3648 -
obs--99.74 %

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