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- PDB-8emg: Crystal structure of a HLA-B*35:01-NP7 epitope from 2002 H2N1 inf... -

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Basic information

Entry
Database: PDB / ID: 8emg
TitleCrystal structure of a HLA-B*35:01-NP7 epitope from 2002 H2N1 influenza strain
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • Nucleoprotein NP7 epitope
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
ACETATE ION / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83001273614 Å
AuthorsLittler, D.R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
Authors: Quinones-Parra, S. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
History
DepositionSep 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP7 epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9454
Polymers44,8863
Non-polymers591
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-28 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.167, 81.925, 110.392
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 MHC class I antigen


Mass: 31940.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: PLASMID / Details (production host): PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4NBT2
#2: Protein Beta-2-microglobulin / 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 / Plasmid: PLASMID / Details (production host): PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein NP7 epitope / Nucleocapsid protein / Protein N


Mass: 1066.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus (strain A/2002/H2N1)
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→26.51 Å / Num. obs: 41590 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 17.025484263 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 4007 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKS

3lks


Resolution: 1.83001273614→26.5092609039 Å / SU ML: 0.159206728737 / Cross valid method: FREE R-VALUE / σ(F): 1.37346989447 / Phase error: 19.0562960228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205591114811 2133 5.12925333654 %
Rwork0.168928875839 39452 -
obs0.170824965487 41585 99.7337874137 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.0844772991 Å2
Refinement stepCycle: LAST / Resolution: 1.83001273614→26.5092609039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 4 441 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01029466985413275
X-RAY DIFFRACTIONf_angle_d1.488275790024451
X-RAY DIFFRACTIONf_chiral_restr0.10498189847454
X-RAY DIFFRACTIONf_plane_restr0.0076143698686588
X-RAY DIFFRACTIONf_dihedral_angle_d21.05396080111230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.831-1.87260.2765766516411260.2282871909122514X-RAY DIFFRACTION96.3152134258
1.8726-1.91940.2139411979221320.1983388959522570X-RAY DIFFRACTION99.9630040696
1.9194-1.97130.1882865649141280.1773801907872653X-RAY DIFFRACTION100
1.9713-2.02930.2110766345841600.1729422275762544X-RAY DIFFRACTION99.8891762098
2.0293-2.09470.2115121591521470.1765066953032616X-RAY DIFFRACTION99.9638205499
2.0947-2.16960.200156409831300.1774487490042608X-RAY DIFFRACTION100
2.1696-2.25640.215596691051450.1761326320092622X-RAY DIFFRACTION99.9638728324
2.2564-2.3590.2053012602661580.1701587102842586X-RAY DIFFRACTION100
2.359-2.48330.2329738681891500.1700056791382632X-RAY DIFFRACTION100
2.4833-2.63880.2282337501851590.1731131365192604X-RAY DIFFRACTION99.9638205499
2.6388-2.84230.2616924284971400.1784503319552646X-RAY DIFFRACTION100
2.8423-3.12790.2099428869541150.1720847414892669X-RAY DIFFRACTION100
3.1279-3.57960.2267552908751470.1595622475562675X-RAY DIFFRACTION100
3.5796-4.50630.1523298248281530.1446552053552678X-RAY DIFFRACTION100
4.5063-26.50.1863742847271430.165478280742835X-RAY DIFFRACTION99.89936263
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)
10.261403630409-0.121635782283-0.0106242263740.212929103632-0.08238806324060.1537869322850.0226469278272-0.03732482885920.1310035173960.009816885865720.003391697458610.0485989003418-0.01837281549-0.02337442268590.004676028427690.0614157317706-0.009498441846290.00970672526460.0621251144802-0.02192256058320.0717177824395-10.3394092654-6.0502996745730.6378045073
20.053295705977-0.004936699883790.06768789225110.548968551911-0.08126449162960.1682089631010.0490199302252-0.1558813618680.08119862319680.323815600407-0.188473886871-0.3834381863780.0356695441382-0.0348078908969-0.1870955214570.151652602843-0.044561189696-0.01104604169650.145788655285-0.0615640258996-0.006741171903670.102309089009-7.0757869846336.3761796949
30.229898377249-0.325077420232-0.1109387016380.2677004255860.1077751150890.166666109842-0.05243318923610.0680412982649-0.196443313485-0.0002359322760830.0370191159233-0.1005860136780.0687668257551-0.054896803819-0.0009748378296030.0516050771631-0.01082370157840.00244011428150.04140924379360.007351844536070.0834913916234-1.71773532816-16.231448358425.3439954637
40.03221157375480.09189154315130.003036934376860.5055309847310.08006901489310.26356800408-0.0192093442564-0.0526823065395-0.1721111808160.090155131051-0.0258097161046-0.1831653552990.04935709620020.00985504746021-0.02419766862430.09378356754580.0010269104183-0.008443687365620.08471556662660.04096499736660.145158931362-0.980666171888-21.699335676431.5161315895
50.3494671993140.01710118508050.1483661229250.493466066806-0.08728035908510.2234891222970.03125765426550.05560777549140.0517715408229-0.2390672546890.1955789285770.2175920195070.3016090402-0.1379936792160.160241144310.162448488379-0.0320140448462-0.05251826248320.142919274240.01699162625160.0796215672771-26.8694742114-13.6762909796.27417538439
60.3330112372060.09932916870780.07129286487380.342595079088-0.06209513201440.3479065524790.173606939390.2185622174570.300282245155-0.02555000133220.1577435284040.3075259029490.444948258269-0.1284830456160.270995649310.119363410576-0.13216094247-0.3540929184880.142271527972-0.0978459512692-0.359173553802-25.7597855521-16.59264428182.02536234521
70.009132364691220.00446073539984-0.001053973860980.0117280223761-0.01426216576410.00944969841805-0.002299895185290.01485911019840.0123523034786-0.04098817881790.0244304070283-0.03463661451320.0241200598481-0.03955624345550.02818607597980.14127213694-0.05895128444570.04632377669430.220119916150.1252434354950.03777934242911.49210944286-5.5459855597910.6702058935
80.01301479200910.001966914635-0.00243623117820.007353726137140.01096840037790.0141073898407-0.05329797625150.04967034566670.0479160480853-0.08758018455480.02206094419250.04850659673340.009938123466040.00190909351155-0.003499896146920.118366378566-0.00483489084715-0.04752150244380.1267650255070.02386141143280.103915550451-17.281317485-2.238834269088.63578893544
90.0571980298614-0.02909305610540.04547307883510.0119552768345-0.02492227363610.0313843435331-0.02515911626840.0131695837630.0363180928469-0.06108784238080.01388413775540.129933794885-0.0538673542077-0.1268502281730.0212775752778-0.06297589791690.0849734725365-0.2592511863290.2107697252540.09635161166310.332964003495-32.50559262872.3927539417610.7806846069
100.0197458266155-0.0120697538275-0.01820642036710.03341232699090.03236402396850.0816734163343-0.2448159430470.02228120532130.2360754098-0.01069766182220.146315713050.0323688030478-0.100221982794-0.02075521595836.14890970985E-50.1272947802060.00839139912121-0.05071179239980.09940521336020.01617654412580.155663177036-13.30445384812.3130065597713.7255736972
110.00281590482309-0.005221179281840.004208047254830.00872540617924-0.0090148594544-0.000510070579447-0.04748438952550.04595739434810.287182320720.05187430901290.04028379381360.0750117468422-0.1973124839210.05512543855660.001455015847590.2685144777060.0237980924229-0.0545499611820.1234228149910.008044521042870.282725843032-17.528092496311.968815901915.8673533046
120.140673933970.106363537342-0.009776309240530.0627347358978-0.004799326238750.090537890358-0.007218831447850.0431933678731-0.047648083327-0.080258550368-0.01365506330770.242391782707-0.002928429099750.0066480617177-0.003716553078220.0724908553156-0.00388890654273-0.02023174635020.079767872073-0.01298646371080.0949279078854-12.9971576256-3.4256683288518.1696714709
130.007439108136980.02144386535350.005901174163140.08792073706880.08827657326930.1327681574620.06871228363060.1348356392950.0985570320438-0.1537244537170.1228542917850.0666980870414-0.105389614065-0.06393094119760.06126925738680.203219462163-0.00863376853646-0.1192008001070.1687261131730.1494791443380.27571894154-20.35947818669.242681386745.95387043158
140.0285909754778-0.0186043997119-0.01514470215140.0200976442115-0.003276736269620.0316876197514-0.0126581766440.1404803963130.0770217570713-0.09531879797260.0409895968611-0.0353656346151-0.030168372629-0.01582288624090.01013365657820.142143983449-0.1357866587140.08189926723590.07394564076520.297225612763-0.016949633128-1.366124482844.121321263816.92381825127
150.04475207631670.000151114596763-0.02479974752250.0357261865748-0.01828683107820.02705850717930.06528665966030.112146610423-0.0261140007856-0.13532573768-0.03325900600890.02023346471840.08517136992230.05090627855840.02148800530320.244539801189-0.0588799155355-0.1515479556340.2165515913040.1247648726270.146644569153-20.16438087412.385885537922.7962388245
160.003325689937-0.0005038139267780.007522390582310.000995924554733-0.002662480807030.002491747572580.0386874401623-0.07380790931190.0714703466540.00875966761867-0.0291693321648-0.106308527721-0.0432052303108-0.07201354326537.62407224069E-60.1363429490640.0025917813363-0.009052658073310.1455480567290.02707446376050.152861435277-0.158557102999-14.782001704437.0550931547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 5 )
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )

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