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- PDB-8emk: Crystal structure of HLA-B*35:01-NP3 epitope from 1957 H2N2 influ... -

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Basic information

Entry
Database: PDB / ID: 8emk
TitleCrystal structure of HLA-B*35:01-NP3 epitope from 1957 H2N2 influenza strain
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP3 epitope
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 EPITOPE / INFLUENZA / INFLUENZA A / T CELL IMMUNITY / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


helical viral capsid / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway ...helical viral capsid / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / viral penetration into host nucleus / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / host cell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont entry into host cell / ribonucleoprotein complex / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66523002948 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.M. / 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
Revision 1.1Oct 16, 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: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP3 epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9285
Polymers44,8823
Non-polymers462
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-40 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.821, 81.523, 109.140
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: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4NBT2
#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 / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein NP3 epitope / Nucleocapsid protein / Protein N


Mass: 1062.302 Da / Num. of mol.: 1 / Fragment: residues 418-426 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (strain A/Singapore/1/1957 H2N2)
References: UniProt: P26072
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: PEG, NA ACETATE

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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: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→43.1 Å / Num. obs: 56575 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 16.3947837952 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.035 / Net I/σ(I): 17.5
Reflection shellResolution: 1.67→1.73 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5266 / CC1/2: 0.902 / Rrim(I) all: 0.294

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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: 1.66523002948→37.1906724331 Å / SU ML: 0.163962894761 / Cross valid method: FREE R-VALUE / σ(F): 1.35136557892 / Phase error: 20.374197021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.206103662857 2661 4.95106612585 %Random selection
Rwork0.178364423801 51085 --
obs0.179734865897 53746 99.7716683064 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7160009398 Å2
Refinement stepCycle: LAST / Resolution: 1.66523002948→37.1906724331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 2 416 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01390298009553257
X-RAY DIFFRACTIONf_angle_d1.510940775544429
X-RAY DIFFRACTIONf_chiral_restr0.0792041339056452
X-RAY DIFFRACTIONf_plane_restr0.00936557403948586
X-RAY DIFFRACTIONf_dihedral_angle_d17.45503856471220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.666-1.69550.2605427778451140.2419274085982599X-RAY DIFFRACTION96.4450764309
1.6955-1.72810.273913158381440.2239957549952629X-RAY DIFFRACTION100
1.7281-1.76340.2457729640531380.2151084794272655X-RAY DIFFRACTION100
1.7634-1.80170.2329910490631340.2071799754422660X-RAY DIFFRACTION99.9284692418
1.8017-1.84360.2579201780221400.2109430161732680X-RAY DIFFRACTION100
1.8436-1.88980.2514204540011380.2032885376242665X-RAY DIFFRACTION100
1.8898-1.94080.2274014582691350.1908234741552667X-RAY DIFFRACTION99.9643239386
1.9408-1.9980.2214412536371410.1869443662262638X-RAY DIFFRACTION99.8921639109
1.998-2.06240.1941331769011260.1832788027652696X-RAY DIFFRACTION99.9291784703
2.0624-2.13610.2261819646611430.1843542659192684X-RAY DIFFRACTION99.9646393211
2.1361-2.22170.2274719832491440.1841423018252638X-RAY DIFFRACTION99.9281609195
2.2217-2.32280.2152408037291420.1784907967592698X-RAY DIFFRACTION100
2.3228-2.44520.2245883094161360.1859210880152682X-RAY DIFFRACTION100
2.4452-2.59840.2485635014341660.1867610735612679X-RAY DIFFRACTION100
2.5984-2.79890.2174920545461640.1871333662582698X-RAY DIFFRACTION100
2.7989-3.08050.2141101906961350.17856128182698X-RAY DIFFRACTION100
3.0805-3.52590.1913767874061270.1651809915522760X-RAY DIFFRACTION100
3.5259-4.44110.1509694306841610.1535906921612741X-RAY DIFFRACTION100
4.4411-37.10.1705972039121330.1572400983842918X-RAY DIFFRACTION99.6082272282
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)
10.0727520213122-0.05581477767190.01079858672270.0519180617699-0.0178828716430.05222834337140.0634703675409-0.03412180764240.07915739748630.0818647160382-0.0449300855790.05115219729460.00918971211347-0.0269683103849-0.002454190287470.0631498996953-0.01296280611530.02326543690090.060753179757-0.0296260827140.0681231442501-10.4509428164-5.517090808330.2676252006
20.3324524762980.2509960612340.1391276670840.6395905310260.0608913995060.2140509429720.0481773080491-0.273552780152-0.2606393408510.224130654838-0.0645200065022-0.3921515558290.0219389639053-0.0508692205903-0.0003076419974570.09637003089-0.0207608762049-0.0312145923790.003031301698340.0207195543420.0636150094222-0.944060732284-15.865466768730.8709642493
30.1748957056660.0229505171190.1561556421290.09178795306340.0830186198940.132097375104-0.04014615969180.07402794657130.0872045712213-0.05285656295350.04555472953050.1921785521340.1817905414060.00470101693989-0.009300096187350.111579324712-0.0405413127656-0.07481337096550.127026935489-0.000546142936350.0420426157272-25.9197048626-15.3574766693.74859607895
40.0602648730137-0.002024063015130.01140296966630.1606781918830.05219139566780.0209254417906-0.08909613822480.005708642904980.0322751836384-0.159399949977-0.01045432533970.130302837543-0.01195099135160.0489072948096-0.004614297591170.144891206921-0.034550362441-0.0255245571860.1426860938340.03348469253830.0607582106077-9.49910412287-3.512227744598.77666286231
50.00266602824129-0.0004957026497670.004603939539640.000149514404888-0.002479857673130.00536509998762-0.01730857123190.01274940572860.000156966865003-0.0139968560267-0.01108819330020.0164058326466-0.0164207622415-0.0262150313906-0.007189325717590.04257715825140.0455132987216-0.1647145834010.218596027090.02252792952520.311568500663-32.55352780162.4202815499710.1369196038
60.03567167921030.00450314375845-0.04010913366460.006415007701170.003379169585680.0742868051741-0.1353113372170.04763911935910.118773777718-0.1580587496070.01074914922150.158964239697-0.1105694055250.0130013631727-0.03874206566610.135192155829-0.00107750183182-0.08101047237250.09556333644340.01648566912790.168759430778-13.39867607352.5929824848513.128837662
70.00253948663396-0.00298904704040.005043767402890.00468619789167-0.007905448802680.01916087879020.0187025522801-0.01472349941540.0163167098763-0.01925400516460.0008230363238490.00211670104485-0.01779606507780.01615711651127.47498996328E-50.265114649512-0.00381776939451-0.1544074377510.1217122583230.03414815231050.278297168062-17.592776393715.31212352589.53633155508
80.00140613780481-0.001298318611190.001531534164490.005153715338060.0002060390543880.000675502829899-0.0182194987245-0.001548038494160.008672082362910.00483491030367-0.02151979628830.00463614376938-0.0191496142076-0.00586698965154-1.35524380288E-50.1886410956930.0255997435914-0.1036512907150.111405379985-0.03753393995270.262334168574-17.50941849259.488235841320.15043523
90.02571365543940.0183996130104-0.02218732943750.00807902618515-0.007900341019260.0492588127748-0.04268070654180.01441331337850.0664840416866-0.08506328444520.02163011545490.1527630392490.0127357378964-0.0519799294669-0.01532715921840.07932373724040.00103103009778-0.04307560531270.0755298529356-0.004298869102130.0979380378178-13.1244010301-3.0792917766117.6688977984
100.0001400914605560.001236036967540.004131939904580.01430849882810.01653266912660.0497031767983-0.0471720086120.06701187874710.0417975036964-0.1803518539280.005848127598430.0874714881902-0.1261241288270.00467385027677-0.009888635975120.215716905462-0.0429348411122-0.08004580174140.1506566904670.08571816289890.204727778629-14.09083467357.758967389855.5034138152
110.00190392228496-0.00110007226191-0.001139028346270.000199010094383-0.001054971338970.003457345768230.007866197465250.0132804724945-0.00250905702656-0.0245401625857-0.01574306429210.00662240280132-0.0258576157020.00987809991554-0.007120876049710.359992190308-0.0492279817646-0.2086313391320.2572071530040.1298533609950.14827782237-20.18554799952.379247370762.18640995813
120.000261945231656-0.00118782483631-0.0004528492785660.000395369200923-0.0007198251832510.00116746441297-0.00484383438465-0.0320826580065-0.007227976552650.0659204442492-0.00421454667104-0.06908133448480.00331184279856-0.02043228557141.33542084991E-60.164801957899-0.0200256414354-0.04371903763120.1720964392920.0316277794910.11859616227-0.20541628361-14.164036489436.7669638019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 56 )A1 - 56
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 57 THROUGH 174 )A57 - 174
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 175 THROUGH 276 )A175 - 276
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 11 )B1 - 11
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 12 THROUGH 19 )B12 - 19
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 20 THROUGH 41 )B20 - 41
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 42 THROUGH 46 )B42 - 46
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 47 THROUGH 51 )B47 - 51
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 52 THROUGH 71 )B52 - 71
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 72 THROUGH 90 )B72 - 90
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 91 THROUGH 99 )B91 - 99
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 1 THROUGH 9 )C1 - 9

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