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- PDB-8umo: Murine CD94-NKG2A receptor in complex with Qa-1b presenting AMAPRTLLL -

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Basic information

Entry
Database: PDB / ID: 8umo
TitleMurine CD94-NKG2A receptor in complex with Qa-1b presenting AMAPRTLLL
Components
  • (Killer cell lectin-like ...) x 2
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-37 alpha chain
  • Qdm peptide
KeywordsIMMUNE SYSTEM / inhibitory receptor / MHC-class I / c-type lectin / transmembrane receptor signalling
Function / homology
Function and homology information


HLA-E specific inhibitory MHC class Ib receptor activity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / MHC class I protein complex binding / 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 ...HLA-E specific inhibitory MHC class Ib receptor activity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / MHC class I protein complex binding / 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 / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / positive regulation of immunoglobulin production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / inner ear development / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of tumor necrosis factor production / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / receptor complex / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / 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 alpha chain, alpha1 alpha2 domains ...Natural killer cell receptor-like, C-type lectin-like domain / 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
BROMIDE ION / Killer cell lectin-like receptor, subfamily D, member 1 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain / H-2 class I histocompatibility antigen, D-37 alpha chain / Killer cell lectin-like receptor subfamily C, member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMacLachlan, B.J. / Rossjohn, J. / Vivian, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: Febs J. / Year: 2024
Title: Structure of the murine CD94-NKG2A receptor in complex with Qa-1 b presenting an MHC-I leader peptide.
Authors: MacLachlan, B.J. / Sullivan, L.C. / Brooks, A.G. / Rossjohn, J. / Vivian, J.P.
History
DepositionOct 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-37 alpha chain
B: Beta-2-microglobulin
J: Killer cell lectin-like receptor, subfamily D, member 1
K: Killer cell lectin-like receptor subfamily C, member 1
P: Qdm peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8626
Polymers72,7825
Non-polymers801
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.170, 65.091, 198.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, D-37 alpha chain


Mass: 32443.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-T23 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P06339
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01887

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Killer cell lectin-like ... , 2 types, 2 molecules JK

#3: Protein Killer cell lectin-like receptor, subfamily D, member 1


Mass: 14130.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrd1 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E9Q3T9
#4: Protein Killer cell lectin-like receptor subfamily C, member 1


Mass: 13517.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrc1 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9WU32

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide Qdm peptide / H-2 class I histocompatibility antigen / L-D alpha chain


Mass: 986.252 Da / Num. of mol.: 1 / Fragment: UNP residues 3-11 / Source method: obtained synthetically / Details: signal peptide from MHC-classI / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P01897

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Non-polymers , 2 types, 102 molecules

#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 23% PEG3350 and 0.2M NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.6→50.46 Å / Num. obs: 21632 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.82 / Num. unique obs: 12725

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50.46 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 1.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.977 / SU Rfree Blow DPI: 0.317 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1112 5.15 %RANDOM
Rwork0.206 ---
obs0.209 21572 99.9 %-
Displacement parametersBiso mean: 67.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.0569 Å20 Å20 Å2
2---5.7655 Å20 Å2
3---4.7086 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.6→50.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 1 101 5135
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037057HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1779SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes873HARMONIC5
X-RAY DIFFRACTIONt_it5196HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion645SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5772SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3102 -6.48 %
Rwork0.2222 404 -
all0.2278 432 -
obs--100 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-17.634322.137-26.0982
2-2.096-7.1437-7.5104
3-0.6487-5.9901-6.64
4-17.2832.8939-5.7798
5-27.88856.3011-7.2042
6-20.60586.4167-8.0888
7-25.1872-2.6043-8.4336
8-29.871450.3366-28.4892
9-39.471739.9106-30.3946
10-42.479630.5345-25.6783
11-33.853939.8976-25.4008
12-15.736346.6897-47.7082
13-7.089240.3435-39.7329
14-0.845543.3644-39.1047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|180 }A1 - 180
2X-RAY DIFFRACTION2{ A|181 - A|227 }A181 - 227
3X-RAY DIFFRACTION3{ A|228 - A|277 }A228 - 277
4X-RAY DIFFRACTION4{ B|1 - B|28 }B1 - 28
5X-RAY DIFFRACTION5{ B|29 - B|50 }B29 - 50
6X-RAY DIFFRACTION6{ B|51 - B|81 }B51 - 81
7X-RAY DIFFRACTION7{ B|82 - B|99 }B82 - 99
8X-RAY DIFFRACTION8{ J|58 - J|99 }J58 - 99
9X-RAY DIFFRACTION9{ J|100 - J|138 }J100 - 138
10X-RAY DIFFRACTION10{ J|139 - J|148 }J139 - 148
11X-RAY DIFFRACTION11{ J|149 - J|178 }J149 - 178
12X-RAY DIFFRACTION12{ K|127 - K|168 }K127 - 168
13X-RAY DIFFRACTION13{ K|169 - K|195 }K169 - 195
14X-RAY DIFFRACTION14{ K|196 - K|215 }K196 - 215

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