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- PDB-3bdw: Human CD94/NKG2A -

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Basic information

Entry
Database: PDB / ID: 3bdw
TitleHuman CD94/NKG2A
Components
  • NKG2-A/NKG2-B type II integral membrane protein
  • Natural killer cells antigen CD94
KeywordsIMMUNE SYSTEM RECEPTOR / NK cells / receptor / Glycoprotein / Lectin / Membrane / Signal-anchor / Transmembrane
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 / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / protein antigen binding ...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 / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / protein antigen binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / DAP12 signaling / carbohydrate binding / adaptive immune response / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / innate immune response / plasma membrane
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 / Roll / Alpha Beta
Similarity search - Domain/homology
NKG2-A/NKG2-B type II integral membrane protein / Natural killer cells antigen CD94
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSullivan, L.C. / Clements, C.S.
CitationJournal: Immunity / Year: 2007
Title: The Heterodimeric Assembly of the CD94-NKG2 Receptor Family and Implications for Human Leukocyte Antigen-E Recognition
Authors: Sullivan, L.C. / Clements, C.S. / Beddoe, T. / Johnson, D. / Hoare, H.L. / Lin, J. / Huyton, T. / Hopkins, E.J. / Reid, H.H. / Wilce, M.C.J. / Kabat, J. / Borrego, F. / Coligan, J.E. / ...Authors: Sullivan, L.C. / Clements, C.S. / Beddoe, T. / Johnson, D. / Hoare, H.L. / Lin, J. / Huyton, T. / Hopkins, E.J. / Reid, H.H. / Wilce, M.C.J. / Kabat, J. / Borrego, F. / Coligan, J.E. / Rossjohn, J. / Brooks, A.G.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Natural killer cells antigen CD94
B: NKG2-A/NKG2-B type II integral membrane protein
C: Natural killer cells antigen CD94
D: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)56,3734
Polymers56,3734
Non-polymers00
Water91951
1
A: Natural killer cells antigen CD94
B: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)28,1862
Polymers28,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
MethodPISA
2
C: Natural killer cells antigen CD94
D: NKG2-A/NKG2-B type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)28,1862
Polymers28,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.651, 34.730, 152.896
Angle α, β, γ (deg.)90.000, 89.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

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
11CYSCYSLEULEUAA58 - 1782 - 122
21CYSCYSLEULEUCC58 - 1782 - 122
12ALAALALYSLYSBB113 - 2321 - 120
22ALAALALYSLYSDD113 - 2321 - 120

NCS ensembles :
ID
1
2

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Components

#1: 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 UNP 57-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRD1, CD94 / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q13241
#2: 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 UNP 113-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRC1, NKG2A / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P26715
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.0M tri-sodium citrate, 0.1M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→76.5 Å / Num. obs: 16457 / Rsym value: 0.122 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.64 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 2242 / Rsym value: 0.219

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B6E

1b6e


Resolution: 2.5→30.59 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 26.382 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 826 5 %RANDOM
Rwork0.234 ---
obs0.236 16445 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 0 51 3922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213992
X-RAY DIFFRACTIONr_bond_other_d0.0010.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9125407
X-RAY DIFFRACTIONr_angle_other_deg0.833.016553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.524.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99815686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4811516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
X-RAY DIFFRACTIONr_nbd_refined0.2140.2784
X-RAY DIFFRACTIONr_nbd_other0.1830.22719
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21834
X-RAY DIFFRACTIONr_nbtor_other0.0860.22138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.268
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.214
X-RAY DIFFRACTIONr_mcbond_it0.4021.53034
X-RAY DIFFRACTIONr_mcbond_other0.0661.5968
X-RAY DIFFRACTIONr_mcangle_it0.5223807
X-RAY DIFFRACTIONr_scbond_it0.78731975
X-RAY DIFFRACTIONr_scangle_it1.1994.51586
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1684TIGHT POSITIONAL0.010.05
1A1684TIGHT THERMAL0.030.5
2B1593TIGHT POSITIONAL0.010.05
2B1593TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 63 -
Rwork0.267 1013 -
all-1076 -
obs--90.42 %
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)
13.1046-0.54-0.03314.26521.42262.93240.0538-0.16770.08730.1786-0.0327-0.18350.06590.0785-0.0211-0.1069-0.00010.0633-0.0945-0.0011-0.1188-11.4592-4.5622-70.744
23.3360.0579-0.18114.11121.45473.02650.03740.205-0.0496-0.19160.0048-0.1348-0.07480.097-0.0423-0.1202-0.0049-0.0555-0.0901-0.0021-0.0852-11.14695.2822-5.69
31.1953-0.744-2.15595.06132.91376.3179-0.008-0.0710.1448-0.0838-0.0646-0.10410.0412-0.33330.07260.0073-0.011-0.03370.1327-0.1073-0.0421-21.522811.0652-49.1285
42.43181.02741.73514.25542.56526.3080.070.0212-0.13940.1534-0.1254-0.0925-0.0853-0.34080.05540.01180.04220.04670.1349-0.117-0.0236-21.4193-10.3692-27.2711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA58 - 1782 - 122
2X-RAY DIFFRACTION2CC58 - 1782 - 122
3X-RAY DIFFRACTION3BB113 - 2321 - 120
4X-RAY DIFFRACTION4DD113 - 2321 - 120

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