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- PDB-9nw6: CA147v24 Fab bound to HLA-E-VL9 -

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Basic information

Entry
Database: PDB / ID: 9nw6
TitleCA147v24 Fab bound to HLA-E-VL9
Components
  • Beta-2-microglobulin
  • CA147v24 heavy chain
  • CA147v24 light chain
  • HLA class I histocompatibility antigen, alpha chain E
  • VL9 peptide
KeywordsIMMUNE SYSTEM / HLA-E / antibody / NKG2a / CD94 / VL9 peptide
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / MHC class Ib protein complex ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 immunoglobulin production / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of interleukin-4 production / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / beta-2-microglobulin binding / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of T cell proliferation / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response
Similarity search - Function
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 / : ...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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWrapp, D. / Hwang, J.K. / Marston, D.J. / Haynes, B.F. / Azoitei, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI164567 United States
CitationJournal: To Be Published
Title: HLA-E-VL9 antibodies mediate NKG2A+ NK cell and CD8+ T cell killing of HIV-infected CD4+ T cells
Authors: Hwang, J.K. / Marston, D.J. / Tuyishime, M. / Yang, H. / Wrapp, D. / Li, D. / Brackenridge, S. / Frazier, M. / Rhodes, B. / Harris, C. / Quastel, M. / Kapingidza, A.B. / Gater, J. / Borrow, ...Authors: Hwang, J.K. / Marston, D.J. / Tuyishime, M. / Yang, H. / Wrapp, D. / Li, D. / Brackenridge, S. / Frazier, M. / Rhodes, B. / Harris, C. / Quastel, M. / Kapingidza, A.B. / Gater, J. / Borrow, P. / Gillespie, G.M. / Ferrari, G. / McMichael, A.J. / Haynes, B.F. / Azoitei, M.L.
History
DepositionMar 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
E: CA147v24 heavy chain
F: VL9 peptide
G: CA147v24 heavy chain
H: CA147v24 light chain
I: CA147v24 light chain
P: VL9 peptide


Theoretical massNumber of molelcules
Total (without water)185,62610
Polymers185,62610
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
G: CA147v24 heavy chain
H: CA147v24 light chain
P: VL9 peptide


Theoretical massNumber of molelcules
Total (without water)92,8135
Polymers92,8135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
E: CA147v24 heavy chain
F: VL9 peptide
I: CA147v24 light chain


Theoretical massNumber of molelcules
Total (without water)92,8135
Polymers92,8135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.680, 92.860, 319.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31728.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Antibody CA147v24 heavy chain


Mass: 24984.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Protein/peptide VL9 peptide / HLA class I histocompatibility antigen / A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 1014.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04439
#5: Antibody CA147v24 light chain


Mass: 23205.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium iodide, 0.1 M MES pH 6.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→92.86 Å / Num. obs: 40717 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 77.21 Å2 / CC1/2: 0.589 / Net I/σ(I): 5.1
Reflection shellResolution: 3.1→3.23 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4528 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→79.81 Å / SU ML: 0.4098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4031
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2583 1994 4.92 %
Rwork0.2392 38528 -
obs0.2401 40522 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.11 Å2
Refinement stepCycle: LAST / Resolution: 3.1→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12854 0 0 0 12854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011413180
X-RAY DIFFRACTIONf_angle_d1.295217907
X-RAY DIFFRACTIONf_chiral_restr0.07051928
X-RAY DIFFRACTIONf_plane_restr0.00872319
X-RAY DIFFRACTIONf_dihedral_angle_d18.38484771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.35131330.34472694X-RAY DIFFRACTION99.44
3.18-3.260.38921430.322684X-RAY DIFFRACTION99.4
3.26-3.360.3651450.30462741X-RAY DIFFRACTION99.59
3.36-3.470.31031340.27772725X-RAY DIFFRACTION99.58
3.47-3.590.25351600.26062673X-RAY DIFFRACTION98.68
3.59-3.740.261380.25932705X-RAY DIFFRACTION99.23
3.74-3.910.26431330.24242739X-RAY DIFFRACTION99.48
3.91-4.110.28091330.24242707X-RAY DIFFRACTION98.07
4.11-4.370.23441420.22142765X-RAY DIFFRACTION99.69
4.37-4.710.21441250.19382760X-RAY DIFFRACTION99.9
4.71-5.180.231430.20332789X-RAY DIFFRACTION99.83
5.18-5.930.24231570.22522776X-RAY DIFFRACTION99.9
5.93-7.460.24851350.25082837X-RAY DIFFRACTION99.4
7.47-79.810.24011730.22812933X-RAY DIFFRACTION98.63

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