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- PDB-3cdg: Human CD94/NKG2A in complex with HLA-E -

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Basic information

Entry
Database: PDB / ID: 3cdg
TitleHuman CD94/NKG2A in complex with HLA-E
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • NKG2-A/NKG2-B type II integral membrane protein
  • Natural killer cells antigen CD94
  • leader peptide of HLA class I histocompatibility antigen, alpha chain G
KeywordsIMMUNE SYSTEM / NK cell receptor / immunity / C-type lectin / MHC / Glycoprotein / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Alternative splicing / Signal-anchor
Function / homology
Function and homology information


natural killer cell mediated immunity / 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 / peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway ...natural killer cell mediated immunity / 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 / peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell tolerance induction / protein antigen binding / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation / positive regulation of endothelial cell apoptotic process / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / filopodium membrane / 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 / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / positive regulation of macrophage cytokine production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / protein homotrimerization / stimulatory C-type lectin receptor signaling pathway / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of interleukin-4 production / MHC class I protein binding / cellular defense response / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / positive regulation of interleukin-12 production / T cell receptor binding / negative regulation of angiogenesis / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 ...Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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-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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
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: 3.4 Å
AuthorsPetrie, E.J. / Clements, C.S. / Lin, J. / Sullivan, L.C. / Johnson, D. / Huyton, T. / Heroux, A. / Hoare, H.L. / Beddoe, T. / Reid, H.H. ...Petrie, E.J. / Clements, C.S. / Lin, J. / Sullivan, L.C. / Johnson, D. / Huyton, T. / Heroux, A. / Hoare, H.L. / Beddoe, T. / Reid, H.H. / Wilce, M.C.J. / Brooks, A.G. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2008
Title: CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence
Authors: Petrie, E.J. / Clements, C.S. / Lin, J. / Sullivan, L.C. / Johnson, D. / Huyton, T. / Heroux, A. / Hoare, H.L. / Beddoe, T. / Reid, H.H. / Wilce, M.C.J. / Brooks, A.G. / Rossjohn, J.
History
DepositionFeb 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,51010
Polymers145,51010
Non-polymers00
Water0
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
J: Natural killer cells antigen CD94
K: NKG2-A/NKG2-B type II integral membrane protein
P: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)72,7555
Polymers72,7555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
E: Natural killer cells antigen CD94
F: NKG2-A/NKG2-B type II integral membrane protein
Q: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)72,7555
Polymers72,7555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)345.201, 345.201, 345.201
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
11A
21C
12J
22E
13K
23F
14B
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTHRTHRchain A and (resseq 2:225 or resseq 227:274 )AA2 - 2251 - 224
121ASPASPTRPTRPchain A and (resseq 2:225 or resseq 227:274 )AA227 - 274226 - 273
211SERSERTHRTHRchain C and (resseq 2:225 or resseq 227:274 )CE2 - 2251 - 224
221ASPASPTRPTRPchain C and (resseq 2:225 or resseq 227:274 )CE227 - 274226 - 273
112ASPASPILEILEchain J and (resseq 57:179 )JC57 - 1791 - 123
212ASPASPILEILEchain E and (resseq 57:179 )EG57 - 1791 - 123
113ALAALALYSLYSchain K and (resseq 113:199 or resseq 204:232 )KD113 - 1991 - 87
123ALAALALYSLYSchain K and (resseq 113:199 or resseq 204:232 )KD204 - 23292 - 120
213ALAALALYSLYSchain F and (resseq 113:199 or resseq 204:232 )FH113 - 1991 - 87
223ALAALALYSLYSchain F and (resseq 113:199 or resseq 204:232 )FH204 - 23292 - 120
114METMETMETMETchain B and (resseq 0:99 )BB0 - 991 - 100
214METMETMETMETchain D and (resseq 0:99 )DF0 - 991 - 100

NCS ensembles :
ID
1
2
3
4

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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: residues in database 23-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin / 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 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein Natural killer cells antigen CD94 / NK cell receptor / Killer cell lectin-like receptor subfamily D member 1 / KP43


Mass: 14431.896 Da / Num. of mol.: 2 / Fragment: residues in database 57-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRD1, CD94 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13241
#4: 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: residues in database 113-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRC1, NKG2A / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P26715
#5: Protein/peptide leader peptide of HLA class I histocompatibility antigen, alpha chain G / HLA G antigen


Mass: 1048.321 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide of the human HLA-G leader sequence
References: UniProt: P17693

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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: 5.889509 Å3/Da / Density % sol: 79.115402 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 48105
Reflection shellHighest resolution: 3.4 Å / Mean I/σ(I) obs: 4.6 / Num. unique all: 6919

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pbd code 3bdw, 3bze

3bdw

3bze


Resolution: 3.4→50 Å / FOM work R set: 0.83 / SU ML: 0.35 / σ(F): 1.38 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 2434 5.06 %
Rwork0.249 --
obs0.25 48093 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.191 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 53.07 Å2 / Biso mean: 119.67 Å2 / Biso min: 367.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10200 0 0 0 10200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610439
X-RAY DIFFRACTIONf_angle_d0.94414122
X-RAY DIFFRACTIONf_chiral_restr0.0661461
X-RAY DIFFRACTIONf_plane_restr0.0031830
X-RAY DIFFRACTIONf_dihedral_angle_d18.8463724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2211X-RAY DIFFRACTIONPOSITIONAL0.023
12C2211X-RAY DIFFRACTIONPOSITIONAL0.023
21J1007X-RAY DIFFRACTIONPOSITIONAL0.022
22E1007X-RAY DIFFRACTIONPOSITIONAL0.022
31K931X-RAY DIFFRACTIONPOSITIONAL0.02
32F931X-RAY DIFFRACTIONPOSITIONAL0.02
41B837X-RAY DIFFRACTIONPOSITIONAL0.02
42D837X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.470.3131410.30926322773100
3.47-3.5450.291430.28926352778100
3.545-3.6270.2761490.26426352784100
3.627-3.7180.2431330.23926682801100
3.718-3.8190.2691380.24526622800100
3.819-3.9310.3041340.23926542788100
3.931-4.0580.2581540.22826472801100
4.058-4.2030.2271390.2226792818100
4.203-4.3710.2261370.20526572794100
4.371-4.570.2381410.19826732814100
4.57-4.8110.2011440.19526792823100
4.811-5.1130.1951540.19326632817100
5.113-5.5070.2451330.21127002833100
5.507-6.0620.2471550.23326972852100
6.062-6.9390.3121370.25827312868100
6.939-8.7420.3071500.26227562906100
8.742-141.0490.3761520.3062891304399
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)
10.09950.0101-0.033-0.0741-0.0434-0.1161-0.0922-0.278-0.01570.11940.03930.0967-0.3696-0.3111-0.076-0.17031.1210.2256-0.0871-0.06650.2536-18.533441.30730.3655
20.01210.00130.0171-0.0278-0.020.0597-0.0424-0.0265-0.14950.06630.0519-0.0289-0.10090.0265-0.07810.42430.44630.29610.265-0.01920.2125-5.50751.318220.525
30.0107-0.0416-0.01640.05580.02670.0428-0.06620.01760.043-0.0302-0.2805-0.11580.03860.1464-0.09460.41580.30430.21950.38720.26510.32730.73888.057140.1252
40.006-0.0031-0.0017-0.00810.01830.0194-0.13880.1127-0.09980.0194-0.1934-0.01760.1514-0.1663-0.01460.51260.06560.34590.6621-0.12290.5509-25.36469.930152.4597
50.01680.0304-0.06470.0107-0.08470.1146-0.0277-0.0853-0.1355-0.0120.08510.1936-0.0325-0.2415-0.11580.29610.30310.13030.44420.31460.4596-33.471825.61788.3576
6-0.0139-0.05310.02170.00250.01470.0252-0.0989-0.0245-0.095-0.16160.195-0.1085-0.0166-0.06250.03950.41570.25630.30910.28770.11320.5594-19.378818.0683-2.0543
7-0.0061-0.0196-0.0038-0.0054-0.0292-0.0254-0.18780.03760.1140.10340.035-0.2236-0.00190.12060.01630.5350.4124-0.22090.610.29560.4504-40.791359.9868-10.1194
80.0114-0.0006-0.01130.0080.00910.022-0.14040.04170.04620.065-0.33160.09960.0399-0.0432-0.00270.53920.37140.1070.724-0.24580.7233-60.952353.41169.735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 274
2X-RAY DIFFRACTION2chain BB0 - 99
3X-RAY DIFFRACTION3chain JJ57 - 179
4X-RAY DIFFRACTION4chain KK113 - 232
5X-RAY DIFFRACTION5chain CC2 - 274
6X-RAY DIFFRACTION6chain DD0 - 99
7X-RAY DIFFRACTION7chain EE57 - 179
8X-RAY DIFFRACTION8chain FF113 - 232

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