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- PDB-1kcg: NKG2D in complex with ULBP3 -

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Basic information

Entry
Database: PDB / ID: 1kcg
TitleNKG2D in complex with ULBP3
Components
  • NKG2-D type II integral membrane protein
  • UL16-binding protein 3
KeywordsIMMUNE SYSTEM / protein-protein complex / C-type lectin-like receptor / MHC class I-like molecule
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / 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 ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / 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 / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / DAP12 signaling / signaling receptor activity / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / cell surface / signal transduction / extracellular space / identical protein binding / membrane / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / 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 ...NKG2-D type II integral membrane protein / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NKG2-D type II integral membrane protein / UL16-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRadaev, S. / Sun, P.
CitationJournal: Immunity / Year: 2001
Title: Conformational plasticity revealed by the cocrystal structure of NKG2D and its class I MHC-like ligand ULBP3.
Authors: Radaev, S. / Rostro, B. / Brooks, A.G. / Colonna, M. / Sun, P.D.
History
DepositionNov 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / software / struct_asym / struct_conn / struct_ref / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
C: UL16-binding protein 3


Theoretical massNumber of molelcules
Total (without water)50,1613
Polymers50,1613
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.050, 62.050, 237.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 14365.250 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 UL16-binding protein 3 / ALCAN-gamma / NKG2D ligand 3 / N2DL-3 / NKG2DL3 / Retinoic acid early transcript 1N


Mass: 21430.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULBP3, N2DL3, RAET1N / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZM4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-15 mg/mlprotein1drop
210 %PEG3350-80001reservoir
350 mMMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9639, 0.9792, 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96391
20.97921
30.97951
ReflectionResolution: 2.6→41 Å / Num. all: 16578 / Num. obs: 16578 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 41 Å / Num. obs: 26678 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 99.9 % / Redundancy: 5.2 % / Num. unique obs: 2683 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
MAR345data collection
HKL-2000data reduction
SOLVEphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→41 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 730 5 %RANDOM
Rwork0.22 ---
all-14728 --
obs-14728 --
Refinement stepCycle: LAST / Resolution: 2.6→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 20 122 3546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.89
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 41 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.49 / Rfactor obs: 0.386

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