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- PDB-8p43: Structure of the MHC class Ib molecule Qa-1b in complex with Q001... -

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Basic information

Entry
Database: PDB / ID: 8p43
TitleStructure of the MHC class Ib molecule Qa-1b in complex with Q001 peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, Qa-1b
  • Q001 peptide
KeywordsIMMUNE SYSTEM / MHC-I 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 / cellular defense response / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...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 / cellular defense response / Neutrophil degranulation / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
Beta-2-Microglobulin / : / 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
NICKEL (II) ION / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSala, B.M. / Achour, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Cancerfondengrant 21 1605 Pj01H Sweden
Swedish Research Councilgrant 2021 05061 Sweden
Other governmentgrant 10399
CitationJournal: To Be Published
Title: MHC-E is a convergent checkpoint ligand for LILRB1 on macrophages and during inflammation for NKG2A on lymphocytes
Authors: Middelburg, J. / Ghaffari, S. / Schoufour, T. / Sluijter, M. / Schaap, G. / Goynuk, B. / Sala, B.M. / Al-Tamimi, L. / Scheeren, F. / Franken, K.L.M.C. / Joosten, S. / Derksen, I. / Neefjes, ...Authors: Middelburg, J. / Ghaffari, S. / Schoufour, T. / Sluijter, M. / Schaap, G. / Goynuk, B. / Sala, B.M. / Al-Tamimi, L. / Scheeren, F. / Franken, K.L.M.C. / Joosten, S. / Derksen, I. / Neefjes, J. / van der Burg, S. / Achour, A. / Wijdeven, R.H.M. / Weidanz, J. / van Hall, T.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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: H-2 class I histocompatibility antigen, Qa-1b
B: Beta-2-microglobulin
P: Q001 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5509
Polymers45,1973
Non-polymers3526
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-48 kcal/mol
Surface area19380 Å2
Unit cell
Length a, b, c (Å)59.560, 72.797, 96.515
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 H-2 class I histocompatibility antigen, Qa-1b


Mass: 32346.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide Q001 peptide


Mass: 1015.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% PEG4000, 0.1M sodium acetate (pH 5.7) and 10 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.43→50.69 Å / Num. obs: 16416 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 42.52 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0337 / Rpim(I) all: 0.0337 / Rrim(I) all: 0.04766 / Net I/σ(I): 13.23
Reflection shellResolution: 2.43→2.517 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2549 / Num. unique obs: 1605 / CC1/2: 0.895 / CC star: 0.972 / Rpim(I) all: 0.2549 / Rrim(I) all: 0.3604 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
AutoProcessdata reduction
TRUNCATEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→50.69 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 823 5.01 %
Rwork0.1912 15593 -
obs0.1939 16416 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.38 Å2
Refinement stepCycle: LAST / Resolution: 2.43→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 6 114 3302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793283
X-RAY DIFFRACTIONf_angle_d0.98584469
X-RAY DIFFRACTIONf_chiral_restr0.0554455
X-RAY DIFFRACTIONf_plane_restr0.0091591
X-RAY DIFFRACTIONf_dihedral_angle_d6.8431434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.33031210.24852548X-RAY DIFFRACTION99.85
2.58-2.780.31621490.24312536X-RAY DIFFRACTION100
2.78-3.060.27441530.21622556X-RAY DIFFRACTION99.96
3.06-3.50.27931330.20612596X-RAY DIFFRACTION100
3.5-4.410.20281210.16762615X-RAY DIFFRACTION99.93
4.41-50.690.2211460.17112742X-RAY DIFFRACTION99.9
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)
11.08871634910.637007378627-0.5922306322750.601025000278-0.4191708736921.71251395299-0.03098888164820.0631377900245-0.093200843302-0.002099950667410.031587960106-0.05277297145080.09531376088330.007982307122913.52625970516E-50.2744256759670.02459177083180.005349683421130.259549720887-0.01499093780490.29497703970721.71727163472.317007543411.6380142214
20.386103301165-0.425557605479-0.2270256294810.740999280054-0.02171058427840.2531431874440.00195958388338-0.1765826189860.0398314163960.0273158499004-0.0531666838662-0.06074717275744.42014445673E-50.01578411863033.14029137998E-50.336873635357-0.0191532428062-0.01121075083640.306594880411-0.01523368516840.3503523056848.5991990107424.394122322325.8884623877
30.3092084150210.192473416570.2637247093020.1030326523070.1238626045470.189009796336-0.3245168638160.3126333074060.0912995548791-0.04017894728580.237503965240.00874057421107-0.314540334644-0.0697545718864-6.9472113529E-50.471779402302-0.07165422865010.00703673482480.4597320189050.003031522984630.37022667151728.063734530119.372699188817.2432009755
40.00544479478920.009529835376380.0007274329550190.011300313423-0.03707278354050.08432710235330.536613852442-0.314100045773-0.125639091887-0.0525345779208-0.1381123761780.192272525569-0.0002974678993850.05145379301950.002249072973360.524666372815-0.0837435061304-0.01594368765570.570165536328-0.001778120103040.37160975205917.670253238712.041226005938.5139179918
50.07448694175210.0951678382790.04447431872040.1047394721020.1010162404810.07718362387530.0649177021646-0.2448820636790.0851601268239-0.194014386027-0.1833463731820.0292177102890.1337387253530.0160802480726-0.0001686995230110.363985945781-0.0246073469136-0.01592434060830.392246191682-0.001200737216750.34392264870324.239858833813.308797654424.2637490949
60.127888898181-0.06499437864010.06729380671420.1115482446560.03261855029690.05906317674850.09876662679370.378056294873-0.4648129089310.1014811728460.249040842411-0.294069080426-0.272862520696-0.1615022622250.01117967384830.3144794284290.0162482588105-0.01520865868850.509788934931-0.01610971512670.35280493589334.407766256112.690992613320.5592502732
70.069141028624-0.0147414281783-0.068712978160.121268951905-0.006023267693720.2565878517610.195156183048-0.420413250539-0.177929669671-0.119607613984-0.310309011497-0.3179810466080.5791211901860.4812567244890.0004425163128910.633025423042-0.0187408254878-0.1230798299560.6444870652630.06842188180620.57541594827533.6853762167.3108205715630.9478824043
80.06763716879110.0572919825780.01776755702540.058149467814-0.02564652474650.0475478280370.19364042426-0.07956860508920.1857940961980.172450915453-0.0901732982187-0.2335181596930.04353770141860.1114135425750.001117045713830.539542160607-0.00805585372221-0.02960396655910.359776361005-0.04106632430210.44209367959723.536543630411.81637237069.43153742349
90.129909361166-0.0165603746219-0.03069532962440.0416020193245-0.03484633005870.03795383243730.0280032873315-0.129129098755-0.280941246198-0.02217316251170.02690691203940.05359501869250.230652010262-0.004565733709760.0001598440664430.458648402017-0.0386571728134-0.05147682765210.407657942749-0.0002854217714810.44024951896725.34679203549.0605635913825.2753734832
100.172209131333-0.04220925156670.1307599407360.263921031644-0.03690781759940.09646098514640.2876279874860.0070183340365-0.09595816798680.258070123501-0.234198099441-0.324043730318-0.04375109040930.3282436537352.44031115184E-50.503109544577-0.152449719616-0.05178869434590.5721571198160.08678730890950.35486721727331.725303808616.04743276632.8583864417
110.00817377027877-0.006356596420140.00281617393460.0285140203951-0.007486695986180.027247967688-0.1804580449640.06344712557460.0465842681621-0.319722705392-0.0619518795796-0.06608061012810.08208319342730.0799246458728-0.0007247716968540.485913103874-0.163874805026-0.04079900441330.923496766094-0.05883131925560.50625450300439.289725926421.458547109517.4669457122
120.0247000829782-0.0503707335286-0.01695206974470.07892745080560.02186206363440.04137687134310.370465100503-0.434104968050.441739345379-0.141179185458-0.04526230549110.105778089057-0.569359982734-0.117168273282-0.0002517708912420.419288724342-0.076686391601-0.02312807129840.568428061073-0.0812823394160.44136071162326.33744742521.020222596832.0184548928
130.05356819066180.03078688422040.01274216497830.01750413457590.0210720741910.050887617967-0.3310080106370.393856862096-0.408296092902-0.0772861741507-0.226665257382-0.3603859810610.157107903850.352955877896-0.001469922910890.3385489796160.02844753820410.01951256313470.3266282123140.02657475037290.35808066385822.7988152921-1.29950274571-4.6325070801
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 277 )AA175 - 277175 - 277
33chain 'B' and (resid 0 through 11 )BB0 - 111 - 12
44chain 'B' and (resid 12 through 19 )BB12 - 1913 - 20
55chain 'B' and (resid 20 through 30 )BB20 - 3021 - 31
66chain 'B' and (resid 31 through 41 )BB31 - 4132 - 42
77chain 'B' and (resid 42 through 51 )BB42 - 5143 - 52
88chain 'B' and (resid 52 through 61 )BB52 - 6153 - 62
99chain 'B' and (resid 62 through 71 )BB62 - 7163 - 72
1010chain 'B' and (resid 72 through 84 )BB72 - 8473 - 85
1111chain 'B' and (resid 85 through 90 )BB85 - 9086 - 91
1212chain 'B' and (resid 91 through 99 )BB91 - 9992 - 100
1313chain 'P' and (resid 1 through 9 )PE1 - 91 - 9

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