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- PDB-9nw8: CA117v2v8 Fab bound to HLA-E-Mtb44 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9nw8
TitleCA117v2v8 Fab bound to HLA-E-Mtb44
Components
  • Beta-2-microglobulin
  • CA117v2v8 heavy chain
  • CA117v2v8 light chain
  • HLA class I histocompatibility antigen, alpha chain E
  • Mtb44 peptide
KeywordsIMMUNE SYSTEM / HLA-E / antibody / NKG2a / CD94 / mycobacterium tuberculosis
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 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 / positive regulation of interleukin-4 production / protection from natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / beta-2-microglobulin binding / MHC class I protein binding / 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 / 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 / negative regulation of neuron projection development / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / receptor ligand activity / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation
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, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
H: CA117v2v8 heavy chain
L: CA117v2v8 light chain
P: Mtb44 peptide


Theoretical massNumber of molelcules
Total (without water)92,4975
Polymers92,4975
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.730, 72.330, 121.270
Angle α, β, γ (deg.)90.000, 101.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 31728.910 Da / Num. of mol.: 1
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.: 1 / 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

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Antibody , 2 types, 2 molecules HL

#3: Antibody CA117v2v8 heavy chain


Mass: 24754.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody CA117v2v8 light chain


Mass: 23153.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein/peptide / Non-polymers , 2 types, 127 molecules P

#5: Protein/peptide Mtb44 peptide


Mass: 980.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium acetate, 20% PEG 3350

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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: Oct 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→61.59 Å / Num. obs: 42884 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.66 Å2 / CC1/2: 0.989 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4178 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→59.45 Å / SU ML: 0.3159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 2055 5.01 %
Rwork0.1959 38947 -
obs0.1983 41002 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 0 126 6516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916556
X-RAY DIFFRACTIONf_angle_d0.89078917
X-RAY DIFFRACTIONf_chiral_restr0.0607969
X-RAY DIFFRACTIONf_plane_restr0.00511148
X-RAY DIFFRACTIONf_dihedral_angle_d25.35492366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.37681480.32612528X-RAY DIFFRACTION93.24
2.35-2.410.30551420.29982562X-RAY DIFFRACTION92.54
2.41-2.480.34871160.2932396X-RAY DIFFRACTION86.53
2.48-2.550.34771300.27992428X-RAY DIFFRACTION88.91
2.55-2.630.27671400.28192671X-RAY DIFFRACTION96.8
2.63-2.730.29221330.26432667X-RAY DIFFRACTION96.35
2.73-2.840.29021300.25522669X-RAY DIFFRACTION96.92
2.84-2.970.3161590.2342652X-RAY DIFFRACTION96.73
2.97-3.120.29131290.23072667X-RAY DIFFRACTION96.61
3.12-3.320.25631520.21592632X-RAY DIFFRACTION94.95
3.32-3.570.24731260.20932466X-RAY DIFFRACTION88.83
3.57-3.930.20571370.17362564X-RAY DIFFRACTION92.79
3.93-4.50.22271340.15422748X-RAY DIFFRACTION97.73
4.5-5.670.18341390.14272674X-RAY DIFFRACTION95.84
5.67-59.450.22571400.16382623X-RAY DIFFRACTION91.55
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.108350135491.4537141503-0.9288827965746.852603190440.3684789718173.22090111756-0.226402286593-0.0227230327023-0.313247937106-0.1583828445880.301784593198-0.550044333810.26574767660.259253082999-0.06617601865410.2811148239380.01612108921590.01766662503590.3636777507890.03123544008440.300738885038-22.9356420764-13.869263590439.4553252781
22.343896419081.66449753791-0.5835952702316.572656495821.34325455811.94733862191-0.1301370705220.4077619209510.299815450148-1.050566893920.1143140845370.516482118971-0.333676368217-0.2609708795520.005200651273520.504358779369-0.00499229994666-0.04130288808710.4576845363080.07295381487420.376948966515-32.7682808756-4.8119599177432.7234431796
35.011449727620.0418064323458-3.867037648754.07672498325-0.08405043416978.399702887440.1571218908820.3560830041020.5249234639740.2670814287370.0126005871490.767578494048-0.419108363808-0.879256066594-0.1339349285220.323383238162-0.01769055106890.0441929363050.4078931573810.102112115880.571822657542-52.0718808675-19.892163321358.7307949008
43.864093673614.14974272578-2.556348284795.39417132689-4.024892639883.47266510070.0748513595175-0.7648677715612.01413093045-1.14266158603-0.2138812005541.46324058199-1.535931368160.0214774825648-0.006490028736010.9275365204110.0311044715355-0.010869497160.499052128168-0.03906576948740.73616145763-31.81586530130.86011626768555.6293975851
56.328103383952.71641652494-0.04817275168584.457424053930.9602135712324.509562071450.0781893946895-1.0625318628-0.4828054364110.1057295316230.2442039915120.109082072417-0.148016024428-0.222773356309-0.2402435482860.378904940794-0.0205212377810.05049141090270.4870367268950.03045799816750.321044265084-36.9585089755-16.211865949361.8440485871
64.15143836511-4.141482355385.14410824734.41204098978-4.364828229019.099476177880.329683984924-0.612022596816-1.78568772172-0.458659407694-0.5973452067330.1699732802911.0539554974-0.1017431178490.101504535370.620238763281-0.0957129522054-0.1045954722120.487208605340.266770230830.819321863034-37.7935863836-31.912480604864.5274634701
73.220010841681.25500652708-0.7297142775338.04382663815-2.363226740793.75195348907-0.00349028118381-0.506340117821-0.222869963528-0.5486767902130.245016596072-0.375190218470.232576420544-0.257665970438-0.4380762918740.451500912578-0.0983917750479-0.01402206361190.4129831277480.09028973012260.414518059915-33.0250042321-18.900083651359.3423480753
81.398144121970.571760186284-0.7955735911325.58920442115-6.075467325596.278246248440.277731939762-0.728717550480.2256229299551.02268608985-0.97690553281-1.0594125204-1.082100568251.06351289011.013950370490.429060518394-0.0618865108568-0.02130119326650.5731654063550.104093203710.482820137622-25.6397462769-11.431622693961.1147080924
97.21723321272-1.470550703690.2187906594737.81547088858-6.199353580145.227016048490.104145561039-0.550592332198-0.2948663038040.690727410593-0.75339535866-1.366724151411.513803947592.571776028930.6138032147550.633086890048-0.0725730757915-0.1070872077210.6139199326240.2669837326010.639660065498-22.651192337-21.371206001265.2058897495
101.824289727773.47415500344-2.962378918577.36841369242-5.289142770417.760854317970.333923741808-0.2070488291110.03151602242270.506787142005-0.423596515492-0.0530211324567-0.0697314701090.322524331433-0.008094034831590.289665278725-0.0213333945912-0.0434249510330.408601203584-0.02204253110350.358289387072-31.1768686769-15.10753272453.0409422411
114.113613236283.31059094248-2.019974555673.62639661759-0.2950359432312.84002028947-0.499859219136-1.001583466910.2813849668771.02663895066-0.2864185052710.07444336681841.25243014016-0.6611809324630.7363090823650.731982042798-0.0409737192768-0.01740918949090.9945704931130.3473764368340.854448698869-33.6177299356-28.499856622175.2514725224
123.87552216460.748720644169-2.245095263763.24384944383-5.212697678878.547888135860.536862419004-1.077177919920.1015800233541.58774639836-0.668958117363-1.62328016805-0.9303050000870.4025649418050.1306212219010.652226446029-0.169183157805-0.07612320685720.5258011985230.02341928988460.485451848359-27.7708108691-8.3564760528266.3664451516
138.372844718135.751914057921.307185142924.289566464611.605364637289.048331845080.458660669535-0.969265746742-0.3411249287081.09293094758-0.6817221235070.205155590305-0.657495466567-0.4752095948880.04887988842630.645594860036-0.06885243803310.09744217608080.7198919695250.08056468425690.487107310922-37.5019096095-18.54381368170.0685188136
145.87552030197-1.31879476549-0.5989533407915.223979724992.925729304187.630795548540.6158615508590.405664002978-0.688916357099-0.5833448598480.768223936218-0.836304678978-1.028244246710.417991030902-1.240814413830.361539397724-0.04198895351440.07984858092580.330081882839-0.04721530407540.4454045500645.74018940006-11.046195497617.5514394863
153.85778357734-0.846010312686-2.743391430992.472741330330.7387306591382.7141207224-0.1103748730660.437753698422-0.247261169758-0.2201969389080.134914415095-0.118686170402-0.203707901066-0.211587839273-0.03679867794290.398750240067-0.104557447832-0.003419758238550.430581061708-0.04376145951080.26804896967-1.53598433707-7.139643151521.1493658718
163.52365177554-2.15977525075-0.4162088914251.402859183711.083827766367.13320661412-0.9415285862930.2257913544460.524114490602-1.114683877460.805242557481-1.43210910127-0.1042022696881.46070077701-0.01656225386051.10611114042-0.1079409418610.3366683935220.5201578141370.03425643060840.9178621924135.75749205928.98897108789-1.726910779
173.871917836752.341033096880.5079982283674.73255674820.3559516796132.80910460942-0.0159893615729-0.140370094803-0.2134536784190.318339572329-0.335831923145-0.336892235908-0.02183222030970.1746314996660.356329831420.991526643527-0.06211889018820.3209694946650.413815848589-0.003358611993720.60060444473328.971962230.7720351238495.50370846832
185.01081710780.55077667929-1.821748404585.95920056944-0.1839001748344.183310555940.1404002841420.09325972947040.747180791348-0.2868027334750.268735560086-0.149118087423-0.872160634467-0.102372977374-0.3829667149880.6978747486280.01463019802210.1816473628210.414723449576-0.02277061132230.419002499092-2.8945285942813.477015632625.4043818416
194.611132198320.705260453479-2.001231061690.610773929619-0.7176154507360.9389216781310.519103491542-0.3008031635430.376051216022-0.205172971206-0.145412421436-0.229380338238-0.4066966991820.115886756315-0.286033865951.01825143508-0.02216665353160.2668582505060.441480461835-0.09142924448180.58601775295918.37013401811.8419180385.50293900577
202.979953030670.883321033770.8604439806194.061993188221.627132653815.113998471330.1570548593990.06073213451450.4406285799930.104320174982-0.2124773849310.393576053414-0.177917324939-0.2772093896030.07286544592380.900777855108-0.006752648472650.3383162087240.412531849152-0.09018351427870.7281240354121.92998224814.2352907705-3.45864611818
217.061958050655.882986628622.111994823415.200069989782.690618652783.208379201280.1223536120620.620538140062-0.824390214601-1.458489236820.138283496093-1.5876321856-0.560126336685-0.0495407738692-0.1689984143920.467616528816-0.02053728378390.1411484066990.4263860740090.08468264299340.450197516546-24.6529214321-7.9695765830.4565100273
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 84 )AA2 - 841 - 83
22chain 'A' and (resid 85 through 174 )AA85 - 17484 - 173
33chain 'A' and (resid 175 through 274 )AA175 - 274174 - 269
44chain 'B' and (resid 1 through 5 )BB1 - 51 - 6
55chain 'B' and (resid 6 through 11 )BB6 - 117 - 12
66chain 'B' and (resid 12 through 19 )BB12 - 1913 - 20
77chain 'B' and (resid 20 through 30 )BB20 - 3021 - 31
88chain 'B' and (resid 31 through 41 )BB31 - 4132 - 42
99chain 'B' and (resid 42 through 51 )BB42 - 5143 - 52
1010chain 'B' and (resid 52 through 71 )BB52 - 7153 - 72
1111chain 'B' and (resid 72 through 77 )BB72 - 7773 - 78
1212chain 'B' and (resid 78 through 90 )BB78 - 9079 - 91
1313chain 'B' and (resid 91 through 99 )BB91 - 9992 - 100
1414chain 'H' and (resid 1 through 17 )HC1 - 171 - 17
1515chain 'H' and (resid 18 through 119 )HC18 - 11918 - 127
1616chain 'H' and (resid 120 through 134 )HC120 - 134128 - 142
1717chain 'H' and (resid 135 through 215 )HC135 - 215143 - 223
1818chain 'L' and (resid 1 through 95B)LD1 - 951 - 99
1919chain 'L' and (resid 96 through 128 )LD96 - 128100 - 133
2020chain 'L' and (resid 129 through 212 )LD129 - 212134 - 217
2121chain 'P' and (resid 1 through 9 )PE1 - 91 - 9

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