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- PDB-1qo3: Complex between NK cell receptor Ly49A and its MHC class I ligand... -

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Basic information

Entry
Database: PDB / ID: 1qo3
TitleComplex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
Components
  • BETA-2-MICROGLOBULIN
  • HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
  • LY49A
  • MHC CLASS I H-2DD HEAVY CHAIN
KeywordsRECEPTOR/IMMUNE SYSTEM / COMPLEX (NK RECEPTOR-MHC CLASS I) / NK CELL / INHIBITORY RECEPTOR / MHC-I / C-TYPE LECTIN-LIKE / HISTOCOMPATIBILITY / B2M / LY49 / LY-49 / RECEPTOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / signaling receptor activity / negative regulation of neuron projection development / carbohydrate binding / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell adhesion / viral protein processing / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / 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) ...Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / 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 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160 / T-cell surface glycoprotein YE1/48
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HUMAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTormo, J. / Mariuzza, R.A.
Citation
Journal: Nature / Year: 1999
Title: Crystal Structure of a Lectin-Like Natural Killer Cell Receptor Bound to its Mhc Class I Ligand
Authors: Tormo, J. / Natarajan, K. / Margulies, D.H. / Mariuzza, R.A.
#1: Journal: Immunity / Year: 1999
Title: Interaction of the Nk Cell Inhibitory Receptor Ly49A with H-2Dd: Identification of a Site Distinct from the Tcr Site.
Authors: Natarajan, K. / Boyd, L.F. / Schuck, P. / Yokoyama, W.M. / Eliat, D. / Margulies, D.H.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Three-Dimensional Structure of H-2Dd Complexed with an Immunodominant Peptide from Human Immunodeficiency Virus Envelope Glycoprotein 120
Authors: Li, H. / Natarajan, K. / Malchiodi, E.L. / Margulies, D.H. / Mariuzza, R.A.
History
DepositionNov 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS I H-2DD HEAVY CHAIN
B: BETA-2-MICROGLOBULIN
C: LY49A
D: LY49A
P: HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1628
Polymers76,9755
Non-polymers1863
Water6,341352
1
C: LY49A
D: LY49A

A: MHC CLASS I H-2DD HEAVY CHAIN
B: BETA-2-MICROGLOBULIN
P: HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1628
Polymers76,9755
Non-polymers1863
Water905
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-13.7 kcal/mol
Surface area30200 Å2
MethodPISA
2
C: LY49A
D: LY49A

A: MHC CLASS I H-2DD HEAVY CHAIN
B: BETA-2-MICROGLOBULIN
P: HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1628
Polymers76,9755
Non-polymers1863
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area9700 Å2
ΔGint-13.7 kcal/mol
Surface area30200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.963, 96.957, 99.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: PROTEIN-PROTEIN COMPLEX BETWEEN THE NK-CELL SURFACE GLYCOPROTEIN DIMERIC AND THE HETEROTRIMER CONSISTING OF THE H-2DD HEAVY CHAIN, THE BETA-2-MICROGLOBULIN AND THE HIV ENVELOPE PEPTIDE. THERE IS A SECOND COMPLEX FORMED THROUGH SITE 2, AS DESCRIBED IN THE MAIN REFERENCE, AND CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW.

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Components

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Protein , 3 types, 4 molecules ABCD

#1: Protein MHC CLASS I H-2DD HEAVY CHAIN / H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN / D-D ALPHA CHAIN / (H-2D(D))


Mass: 32265.902 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Gene: H-2D / Plasmid: PET3A / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein BETA-2-MICROGLOBULIN / B2M


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57BL/6 / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Plasmid: PET21D / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein LY49A / NK-CELL SURFACE GLYCOPROTEIN YE1/48 / T LYMPHOCYTE ANTIGEN A1 / LY49-A ANTIGEN / LY49A


Mass: 15921.329 Da / Num. of mol.: 2 / Fragment: C-TYPE LECTIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57BL/6 / Cell: NATURAL KILLER CELLS SOME T CELLS / Cellular location: CELL SURFACE / Plasmid: PET21A / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20937

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Protein/peptide , 1 types, 1 molecules P

#4: Protein/peptide HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE


Mass: 1075.265 Da / Num. of mol.: 1 / Fragment: RESIDUES 318-327 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: P04582

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Non-polymers , 2 types, 355 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNATURAL VARIANTS ARISE FROM STRAIN C57BL/6

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Ly49A NKD : H-2Dd = 1.5:1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlLy49A NKD1drop
320 mMHEPES1drop
4100 mM1dropNaCl
59 %mPEG5501reservoir
650 mMmagnesium acetate1reservoir
7100 mMMES1reservoir
2H-2Dd1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 33230 / % possible obs: 94.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.053 / Net I/σ(I): 15.14
Reflection shellResolution: 2.3→2.35 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.161 / % possible all: 80.7
Reflection
*PLUS
Num. measured all: 128909 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 80.7 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1B6E, 1DDH

1b6e

1ddh


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1971 6 %RANDOM
Rwork0.198 ---
obs0.198 32986 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28 Å2 / ksol: 0.340658 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---3.36 Å20 Å2
3---3.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5178 0 12 352 5542
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 233 5.8 %
Rwork0.204 3755 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ETH.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMETH.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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