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- PDB-3cii: Structure of NKG2A/CD94 bound to HLA-E -

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Basic information

Entry
Database: PDB / ID: 3cii
TitleStructure of NKG2A/CD94 bound to HLA-E
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen peptide
  • HLA class I histocompatibility antigen, alpha chain E
  • NKG2-A/NKG2-B type II integral membrane protein
  • Natural killer cells antigen CD94
KeywordsIMMUNE SYSTEM / C-type lectin-like / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Lectin / Receptor / Signal-anchor
Function / homology
Function and homology information


inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / natural killer cell mediated immunity / peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation ...inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / natural killer cell mediated immunity / peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / MHC class I protein complex binding / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / regulation of natural killer cell activation / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / negative regulation of immune response / positive regulation of T cell tolerance induction / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / negative regulation of G0 to G1 transition / protein antigen binding / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / positive regulation of macrophage cytokine production / positive regulation of regulatory T cell differentiation / 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 / positive regulation of immunoglobulin production / CD8 receptor binding / positive regulation of interleukin-4 production / beta-2-microglobulin binding / stimulatory C-type lectin receptor signaling pathway / protein homotrimerization / positive regulation of natural killer cell proliferation / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of endothelial cell apoptotic process / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of angiogenesis / 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 / 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 / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system
Similarity search - Function
: / 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, alpha chain, C-terminal / MHC_I C-terminus ...: / 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, alpha chain, C-terminal / MHC_I C-terminus / 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 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
HLA class I histocompatibility antigen, alpha chain E / HLA class I histocompatibility antigen, alpha chain G / NKG2-A/NKG2-B type II integral membrane protein / Beta-2-microglobulin / Natural killer cells antigen CD94
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.41 Å
AuthorsStrong, R.K. / Kaiser, B.K. / Pizarro, J.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis for NKG2A/CD94 recognition of HLA-E.
Authors: Kaiser, B.K. / Pizarro, J.C. / Kerns, J. / Strong, R.K.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 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.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen peptide
D: HLA class I histocompatibility antigen, alpha chain E
E: Beta-2-microglobulin
F: HLA class I histocompatibility antigen peptide
G: Natural killer cells antigen CD94
H: NKG2-A/NKG2-B type II integral membrane protein
I: Natural killer cells antigen CD94
J: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)145,07310
Polymers145,07310
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen peptide
G: Natural killer cells antigen CD94
H: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)72,5375
Polymers72,5375
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class I histocompatibility antigen, alpha chain E
E: Beta-2-microglobulin
F: HLA class I histocompatibility antigen peptide
I: Natural killer cells antigen CD94
J: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)72,5375
Polymers72,5375
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)345.983, 345.983, 345.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21I
12A
22D
13A
23D
14B
24E
15C
25F
16H
26J

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSILEILEGG59 - 1791 - 121
21CYSCYSILEILEII59 - 1791 - 121
12SERSERHISHISAA2 - 1811 - 180
22SERSERHISHISDD2 - 1811 - 180
13LEULEUTRPTRPAA182 - 274181 - 273
23LEULEUTRPTRPDD182 - 274181 - 273
14METMETMETMETBB0 - 991 - 100
24METMETMETMETEE0 - 991 - 100
15VALVALLEULEUCC1 - 91 - 9
25VALVALLEULEUFF1 - 91 - 9
16HISHISLYSLYSHH115 - 2323 - 120
26HISHISLYSLYSJJ115 - 2323 - 120

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31640.803 Da / Num. of mol.: 2 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide HLA class I histocompatibility antigen peptide


Mass: 1048.321 Da / Num. of mol.: 2 / Fragment: peptide presented by HLA-E (UNP residues 3-11) / Source method: obtained synthetically
Details: peptide is naturally found in humans and was chemically synthesized.
References: UniProt: P17693
#4: Protein Natural killer cells antigen CD94 / NK cell receptor / Killer cell lectin-like receptor subfamily D member 1 / KP43


Mass: 14213.664 Da / Num. of mol.: 2 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRD1, CD94 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q13241
#5: Protein NKG2-A/NKG2-B type II integral membrane protein / NKG2-A/B-activating NK receptor / NK cell receptor A / CD159a antigen


Mass: 13754.549 Da / Num. of mol.: 2 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRC1, NKG2A / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P26715
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: 5.95 Å3/Da / Density % sol: 79.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 4.41→70 Å / Num. obs: 22619 / % possible obs: 100 % / Redundancy: 34.4 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.9
Reflection shellResolution: 4.4→4.56 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.03 / Num. unique all: 2189 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KPR, 1B6E

1kpr

1b6e


Resolution: 4.41→67.88 Å / Cor.coef. Fo:Fc: 0.753 / Cor.coef. Fo:Fc free: 0.68 / SU B: 136.822 / SU ML: 0.792 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35529 1155 5.1 %RANDOM
Rwork0.32054 ---
all-22600 --
obs-21445 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.161 Å2
Refinement stepCycle: LAST / Resolution: 4.41→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10146 0 0 0 10146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02110444
X-RAY DIFFRACTIONr_bond_other_d0.0020.027140
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.92414172
X-RAY DIFFRACTIONr_angle_other_deg0.843.00517202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20251226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60123.818550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.979151734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2921570
X-RAY DIFFRACTIONr_chiral_restr0.0660.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022236
X-RAY DIFFRACTIONr_nbd_refined0.2090.21743
X-RAY DIFFRACTIONr_nbd_other0.2050.27000
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24537
X-RAY DIFFRACTIONr_nbtor_other0.0820.25879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.25
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0891.58012
X-RAY DIFFRACTIONr_mcbond_other0.0291.52487
X-RAY DIFFRACTIONr_mcangle_it0.12629970
X-RAY DIFFRACTIONr_scbond_it0.16835161
X-RAY DIFFRACTIONr_scangle_it0.2514.54202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1G581tight positional0.020.05
2A2551tight positional0.020.05
3A1253tight positional0.020.05
4B1434tight positional0.040.05
5C125tight positional0.010.05
6H1563tight positional0.030.05
1G581tight thermal0.020.5
2A2551tight thermal0.010.5
3A1253tight thermal0.010.5
4B1434tight thermal0.010.5
5C125tight thermal0.010.5
6H1563tight thermal0.010.5
LS refinement shellResolution: 4.405→4.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 72 -
Rwork0.277 1566 -
obs-1566 100 %
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)
19.4742-1.19943.43446.7812-1.62511.45940.1579-0.2827-0.3217-0.4918-0.2525-0.79331.26320.97140.0946-0.59320.41330.3772-0.41860.5879-0.6541-138.1577158.0803-141.7246
213.34341.8019-4.31539.5762-2.13511.73860.3267-0.9107-0.93731.6567-0.69920.09921.2166-0.41910.37250.07870.32160.0843-0.15510.5574-0.4682-151.3496148.5411-109.2287
35.8509-0.00872.254911.42086.704111.2046-0.4976-0.0026-0.6319-0.1050.17541.15380.77570.510.3221-0.21490.11350.4664-0.88120.5326-0.372-167.9537135.312-135.9187
48.66042.0358-2.485916.4566-3.98882.0117-0.43231.4116-0.3129-1.93490.0244-0.6839-0.08220.85160.40791.3416-0.1812-0.0441-0.14540.1977-0.5832-157.7852149.317-167.8697
57.6895-1.21970.80510.76084.594820.1139-0.5536-0.99450.4660.90210.18270.1386-0.7230.93080.3709-0.52970.40090.104-0.52970.4828-0.6937-152.2144168.0255-120.8441
69.8842-0.18236.22631.8838-0.722619.1675-0.80640.9594-0.2522-1.5937-0.05831.0088-1.2056-0.8950.86470.45210.2953-0.3566-0.66610.24360.0021-175.1451154.0327-154.001
720.4251-4.9076-4.002713.445-3.593510.37250.2184-0.21980.4261-0.45830.35620.10660.02290.6765-0.5746-0.80930.16960.2034-0.72060.3029-0.9339-132.7216173.9532-163.9925
88.5701-0.7117-1.457317.2058-1.93959.04910.0722-0.45260.29150.4903-0.21610.2407-0.0513-0.20810.1439-0.30580.05320.5288-0.54720.2073-0.3119-182.6791132.2677-112.3409
99.5002-2.68253.689921.5069-6.304114.81650.1885-0.2165-0.1476-0.255-0.0812-0.2674-0.2207-0.8718-0.1073-0.74320.34560.271-0.6250.1135-0.4983-121.2097147.3754-161.5577
1019.2712-5.2344-6.627410.49584.44519.7950.23760.101-0.2965-0.09970.32860.5818-0.0552-0.5179-0.5662-0.1656-0.0064-0.0151-0.74330.5051-0.5243-162.2208112.5905-119.5548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 181
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A182 - 274
4X-RAY DIFFRACTION3D2 - 181
5X-RAY DIFFRACTION3F1 - 9
6X-RAY DIFFRACTION4D182 - 274
7X-RAY DIFFRACTION5B0 - 99
8X-RAY DIFFRACTION6E0 - 99
9X-RAY DIFFRACTION7G59 - 179
10X-RAY DIFFRACTION8I59 - 179
11X-RAY DIFFRACTION9H115 - 232
12X-RAY DIFFRACTION10J115 - 232

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