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- PDB-1hyr: CRYSTAL STRUCTURE OF HUMAN MICA IN COMPLEX WITH NATURAL KILLER CE... -

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Basic information

Entry
Database: PDB / ID: 1hyr
TitleCRYSTAL STRUCTURE OF HUMAN MICA IN COMPLEX WITH NATURAL KILLER CELL RECEPTOR NKG2D
Components
  • MHC CLASS I CHAIN-RELATED PROTEIN A
  • NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
KeywordsIMMUNE SYSTEM / ACTIVATING NK CELL RECEPTOR / NKG2D / C-TYPE-LECTIN LIKE / MIC-A / MHC-I / COMPLEX
Function / homology
Function and homology information


immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell activation ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / negative 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 / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / 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 / response to heat / carbohydrate binding / defense response to virus / killing of cells of another organism / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / receptor ligand activity / external side of plasma membrane / DNA damage response / cell surface / signal transduction / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NKG2-D type II integral membrane protein / MHC class I polypeptide-related sequence A / MHC class I polypeptide-related sequence A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLi, P. / Strong, R.K.
Citation
Journal: Nat.Immunol. / Year: 2001
Title: Complex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA.
Authors: Li, P. / Morris, D.L. / Willcox, B.E. / Steinle, A. / Spies, T. / Strong, R.K.
#1: Journal: Immunity / Year: 1999
Title: Crystal Structure of the MHC Class I Homolog Mic-A, a Gammadelta T Cell Ligand
Authors: Li, P. / Willie, S.T. / Bauer, S. / Morris, D.L. / Spies, T. / Strong, R.K.
#2: Journal: Science / Year: 1999
Title: ACTIVATION OF NK CELLS AND T CELLS BY NKG2D, A RECEPTOR FOR STRESS INDUCIBLE MICA
Authors: Bauer, S. / Groh, V. / Wu, J. / Steinle, A. / Phillips, J.H. / Lanier, L.L. / Spies, T.
History
DepositionJan 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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
B: NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
A: NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
C: MHC CLASS I CHAIN-RELATED PROTEIN A


Theoretical massNumber of molelcules
Total (without water)63,4313
Polymers63,4313
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-18 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.780, 122.780, 101.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN / NKG2D


Mass: 15849.903 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN (RESIDUES 80 TO 216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CELL SURFACE / Gene: NKG2D / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26718
#2: Protein MHC CLASS I CHAIN-RELATED PROTEIN A / MIC-A / MIC / PERB11


Mass: 31731.434 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (RESIDUES 1 TO 274)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICA-001 / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9TQ92, UniProt: Q29983*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
225 mMPIPES1drop
31 mMEDTA1drop
40.02 %1dropNaN3
50.4 Mammonium sulfate1reservoir
650 mMMES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 5.0.211.11.1
SYNCHROTRONALS 5.0.220.9794, 0.9795, 0.9567
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.11
30.97941
40.97951
50.95671
ReflectionResolution: 2.7→30 Å / Num. all: 256599 / Num. obs: 21938 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 34
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2150 / Rsym value: 0.425 / % possible all: 100
Reflection
*PLUS
Num. measured all: 256599 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→29.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 185946.74 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1553 7.4 %RANDOM
Rwork0.227 ---
all0.227 21938 --
obs0.227 21108 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.93 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.43 Å20 Å20 Å2
2---5.43 Å20 Å2
3---10.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 0 46 4309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 243 7.5 %
Rwork0.346 2981 -
obs--90.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.397 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.346

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