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- PDB-8tqa: Crystal structure of Fab.28.14.8 in complex with MHC-I (H2-Db) -

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Basic information

Entry
Database: PDB / ID: 8tqa
TitleCrystal structure of Fab.28.14.8 in complex with MHC-I (H2-Db)
Components
  • Beta-2-microglobulin
  • Fab.28.14S Heavy chain
  • Fab.28.14S Light Chain
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • influenza peptide
KeywordsIMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / 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 / peptide binding / 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 / 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 / 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 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 / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Immunol. / Year: 2024
Title: Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
Authors: Boyd, L.F. / Jiang, J. / Ahmad, J. / Natarajan, K. / Margulies, D.H.
History
DepositionAug 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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-B alpha chain
B: Beta-2-microglobulin
H: Fab.28.14S Heavy chain
L: Fab.28.14S Light Chain
P: influenza peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57017
Polymers91,6065
Non-polymers96412
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-20 kcal/mol
Surface area35940 Å2
Unit cell
Length a, b, c (Å)71.387, 70.185, 94.340
Angle α, β, γ (deg.)90.000, 98.000, 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 H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 31804.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab.28.14S Heavy chain


Mass: 23396.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 28.14S / Production host: Mus musculus (house mouse)
#4: Antibody Fab.28.14S Light Chain


Mass: 23719.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 28.14S / Production host: Mus musculus (house mouse)

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Protein/peptide / Sugars , 2 types, 2 molecules P

#5: Protein/peptide influenza peptide


Mass: 1026.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 77 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG4000, 0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→60.57 Å / Num. obs: 28484 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.83 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Net I/σ(I): 13.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2837 / CC1/2: 0.855 / CC star: 0.963 / Rpim(I) all: 0.276 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WBX

1wbx


Resolution: 2.6→60.57 Å / SU ML: 0.4007 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.4539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 1425 5 %
Rwork0.1813 27059 -
obs0.1848 28484 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 62 66 6430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896526
X-RAY DIFFRACTIONf_angle_d1.07548864
X-RAY DIFFRACTIONf_chiral_restr0.0591950
X-RAY DIFFRACTIONf_plane_restr0.00841134
X-RAY DIFFRACTIONf_dihedral_angle_d17.19442326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.3891400.2672660X-RAY DIFFRACTION97.66
2.69-2.80.32851410.24372678X-RAY DIFFRACTION98.74
2.8-2.920.36121420.24062691X-RAY DIFFRACTION98.54
2.92-3.080.29551410.21782686X-RAY DIFFRACTION98.92
3.08-3.270.26841430.19832717X-RAY DIFFRACTION99.58
3.27-3.520.28461430.19462705X-RAY DIFFRACTION99.48
3.52-3.880.24451420.16912698X-RAY DIFFRACTION98.92
3.88-4.440.21251410.1512697X-RAY DIFFRACTION98.17
4.44-5.590.19391450.13912749X-RAY DIFFRACTION99.38
5.59-60.570.21331470.16782778X-RAY DIFFRACTION98.68
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)
12.6821261934-5.170714162820.8682232987782.00397014747-1.732461159280.8211796586790.0804676761330.398150993083-0.5112852214840.295853136115-0.3397762966440.82195088411-0.2131464730510.2605615479380.3220702021810.4987604472510.0280148610307-0.08195466889720.3632335125270.01441620607320.503767251721-24.373166194418.3575294656-56.1144133158
22.88486307853-0.03098612122010.2945787664723.912201163860.1176228517793.411642863090.04689084082360.281358508571-0.0127377322479-0.3762158224970.0491821775746-0.1885143531590.01518779397690.430163050523-0.09033479391850.199740847594-0.0277804850075-0.03529518334890.2501546681530.001186291714580.213089114613-13.191809252615.8300641008-55.8566887817
31.48154898961-0.06854474467430.4999374223352.91830104582-0.5666703846231.976149183330.146136349431-0.1358564290240.1281815666360.337379876706-0.1999230195710.455908673748-0.129096273857-0.1330771521940.02945169029830.447386209687-0.0246723932368-0.01191392398650.147002761391-0.004951330331270.352458218661-25.923575308421.1833193057-45.3636486554
44.601573969713.130541551423.457006355272.039209366412.620447226292.76085619020.02478925915790.494802497392-1.053442923390.0925830917220.273278459660.1103019443830.09893947886180.427924109523-0.3206314320110.503478020558-0.04456320767260.06096962685050.227985773947-0.005366316065190.444235283045-14.43598413081.05586645516-44.0537344491
54.360207283161.277948682671.122522856441.500803569611.279258627525.21290160880.00973204692910.135005171816-0.127502863417-0.0136567430813-0.0145880477372-0.2438306570620.209216237090.7434428775080.04239217471440.23973966240.113532944240.05506339142090.3194660982730.09959792187820.3104047292889.3172167176615.9518249434-24.4532398608
65.328532384651.958017788860.4494392881383.487927786010.7932758824675.33191056059-0.6008168245490.05362963437520.191559344430.07985039763480.497896598096-0.4138808331110.09258432346011.3911477680.2050130761140.32169376105-0.103048442351-0.02014037423690.8273640975470.0665013491710.28195221420510.874986756417.833351761-42.4671821051
75.270618461210.4542408604850.04850855605261.24648569378-0.1936322577750.552481797883-0.2871930464430.1976230316480.041613524571-0.3737035185890.240011525752-0.183503639264-0.4323503516951.293003646640.139793063940.56931397736-0.182891610130.008483617921630.771512550010.05120133404580.3226729788975.4073792209721.7739163618-50.9433883768
84.515087706062.150634145341.102593513931.044585846830.5736904101522.65339210102-0.4920337361690.5830747176890.1330732187260.0155030846950.410898802607-0.425545086456-0.4957773757651.205913074530.1877301852630.469804405644-0.2563276698220.03160331213350.926159480920.0842147127950.49074335537313.888014172122.5828076419-45.5127090985
95.40478845842-0.00702353129587-0.5989150614290.5924382956730.4927837078812.09457547461-0.08075104739420.0799070625947-0.0250827945847-0.04491108167830.001969873672650.09471370159940.0795702529956-0.2991085103870.06322825944360.1932427061810.01196441870410.004988684938120.2033798144840.01130759926140.21536389058-18.60919019516.6832575383-19.1651408323
105.147516049950.313581835861.447669344162.4771613956-1.25402653435.91591653111-0.0620904089109-0.3326047386090.5691699948340.3249937187110.09278204589960.411676518482-0.477154760398-0.0244339460993-0.07298145480440.2785458058710.007711015390380.02053349635160.213180339387-0.02489694255090.34702057488-44.376714139622.45080746565.96525512505
112.84355195385-0.389082727574-1.946519921772.628315934033.262267216665.487500575850.045300753566-1.47408577508-0.6028371001640.6680521828170.0795838646713-0.3894661383680.9635082952020.297826209436-0.007593485844060.4748751967590.0294997736846-0.001136800797060.758467037550.1661097834340.307598368969-9.143160757378.415736735024.29328875199
123.002068676421.67412400812-0.2597954917942.048792167830.2997323247543.716829115440.102516627716-0.662547148014-0.03948488006040.328028191961-0.127702459789-0.2678170954260.1058190646830.5549303221110.05091344949610.245158546121-0.03878056210630.01936208869630.5024040277290.09746473050120.260360799521-4.0234621204615.2522987377-2.80244266417
132.189235390540.530797872435-3.071071809530.535181930642-0.9629353085253.31753242120.248692654119-0.6893549192970.1063792291810.126561912999-0.0488288549725-0.2400742797510.03186421050270.588380320348-0.1428142746970.276669920184-0.0146037844311-0.03515511998180.5856822582490.06698605880860.315288827653-13.142888241813.40883618312.41468529921
144.530489024630.53180813410.7183939603162.25665011713-0.5603366541923.724441928430.143111084824-0.129348065517-0.0326157098137-0.0873967176580.145388953730.3578755900210.134868074786-0.0597672062505-0.283725903730.31813205408-0.05722506575510.01704024273840.2686055281230.002816462148690.28123819596-42.76680643629.9139908123210.0970170572
153.884604009490.863759331261-0.4532840697923.01324273325-1.694690451323.065469434030.2289860172480.178202073921-0.485975253505-0.0845552922360.1058660052120.2141653007430.69276813240.0218021787143-0.245216659340.5103866169440.0640386480893-0.09233226974860.443894603731-0.07114525660980.356345038246-41.99373758791.838474066425.26336545155
163.26010112847-0.9416830696181.011325460282.34009151372-0.6642791972133.748627872060.126017860386-0.341121114497-0.3635295823750.141173538740.05488124383550.4107891238530.374809675122-0.333136910458-0.1921425513260.39565854773-0.0481114050941-0.004015580096490.3892785507620.02954556387390.264035456713-42.65241098197.3122921779512.1184202243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'P' and (resid 1 through 9 )PF1 - 91 - 9
22chain 'A' and (resid 2 through 103 )AA2 - 1031 - 102
33chain 'A' and (resid 104 through 161 )AA104 - 161103 - 160
44chain 'A' and (resid 162 through 185 )AA162 - 185161 - 180
55chain 'A' and (resid 186 through 274 )AA186 - 274181 - 269
66chain 'B' and (resid 2 through 30 )BB2 - 301 - 29
77chain 'B' and (resid 31 through 61 )BB31 - 6130 - 60
88chain 'B' and (resid 62 through 99 )BB62 - 9961 - 98
99chain 'H' and (resid 1 through 122 )HC1 - 1221 - 122
1010chain 'H' and (resid 123 through 217 )HC123 - 217123 - 214
1111chain 'L' and (resid 1 through 25 )LE1 - 251 - 25
1212chain 'L' and (resid 26 through 75 )LE26 - 7526 - 75
1313chain 'L' and (resid 76 through 113 )LE76 - 11376 - 113
1414chain 'L' and (resid 114 through 150 )LE114 - 150114 - 150
1515chain 'L' and (resid 151 through 163 )LE151 - 163151 - 163
1616chain 'L' and (resid 164 through 213 )LE164 - 213164 - 213

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