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- PDB-9aud: Immune receptor complex -

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Basic information

Entry
Database: PDB / ID: 9aud
TitleImmune receptor complex
Components
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • NPLCK1-2 TCR TRBV1 Beta chain
  • NPLCK1-2_TCR TRAV6-5 alpha chain
  • Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain
KeywordsIMMUNE SYSTEM / peptide HLA complex / IMMUNE SYSTEM-VIRAL peptide complex
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / helical viral capsid / antigen processing and presentation / response to type II interferon ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / helical viral capsid / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / viral penetration into host nucleus / host cell / viral nucleocapsid / adaptive immune response / early endosome / lysosome / immune response / ribonucleoprotein complex / symbiont entry into host cell / external side of plasma membrane / ubiquitin protein ligase binding / host cell nucleus / structural molecule activity / Golgi apparatus / RNA binding / membrane / plasma membrane
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
Nucleoprotein / H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus H3N2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChaurasia, P. / Littler, D.R. / La Gruta, N. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To be published
Title: NP-LCK2-1TCR-MHC complex
Authors: Zhang, J.B. / Chaurasia, P. / Littler, D.R. / La Gruta, N. / Rossjohn, J.
History
DepositionFeb 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain
A: NPLCK1-2_TCR TRAV6-5 alpha chain
B: NPLCK1-2 TCR TRBV1 Beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,13612
Polymers98,3224
Non-polymers8158
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.344, 196.344, 77.104
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Protein , 4 types, 4 molecules CDAB

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 21204.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expression tag on C terminal residue 181-188 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14434
#2: Protein Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain / Nucleocapsid protein / Protein N


Mass: 26266.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from ...Details: Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from construct, not present in electron density.,Residue -25 to -11 (1-15 aligned sequence) QVYSLIRPNENPAHK- NP311-325, Flu peptide sequence. Residue GSGGSIEGRGGSGASGDS (16-34 aligned sequence) is unique peptide linker sequence from construct, not present in electron density.
Source: (gene. exp.) Influenza A virus H3N2, (gene. exp.) Mus musculus (house mouse)
Gene: NP, H2-Ab1, H2-iabeta / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O92607, UniProt: P14483
#3: Protein NPLCK1-2_TCR TRAV6-5 alpha chain


Mass: 23039.350 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)
#4: Protein NPLCK1-2 TCR TRBV1 Beta chain


Mass: 27811.383 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)

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Sugars , 1 types, 2 molecules

#6: 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.: 2 / 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 , 2 types, 48 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium Acetate, 0.1 M BIS-TRIS prop pH 8.5, 20 %w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.9→49.37 Å / Num. obs: 24545 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 67.46 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Net I/σ(I): 11
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4 / Num. unique obs: 3973 / CC1/2: 0.775 / Rpim(I) all: 0.169 / Rrim(I) all: 0.366 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.37 Å / SU ML: 0.3399 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.0546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 1286 5.24 %
Rwork0.1829 23250 -
obs0.1847 24536 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6059 0 52 42 6153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196306
X-RAY DIFFRACTIONf_angle_d0.45348610
X-RAY DIFFRACTIONf_chiral_restr0.0434970
X-RAY DIFFRACTIONf_plane_restr0.00351112
X-RAY DIFFRACTIONf_dihedral_angle_d11.28092197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.020.32291350.25032559X-RAY DIFFRACTION99.96
3.02-3.150.25061310.23092594X-RAY DIFFRACTION100
3.15-3.320.28211320.23352618X-RAY DIFFRACTION99.96
3.32-3.530.2471480.19772572X-RAY DIFFRACTION100
3.53-3.80.20521660.18862561X-RAY DIFFRACTION100
3.8-4.180.22281470.18572586X-RAY DIFFRACTION100
4.18-4.790.17371450.14262598X-RAY DIFFRACTION100
4.79-6.030.2081470.16432565X-RAY DIFFRACTION100
6.03-49.370.20021350.18172597X-RAY DIFFRACTION99.78
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)
16.436607079273.173705590131.238938156258.271299343541.220187481722.09664885621-0.173323189710.4640405985830.14823003302-0.08857759180470.1653967900750.170713745327-0.1480923997760.1873867459390.02335154365330.2574008256010.02580577774380.03538234694050.4532508840210.06276163633750.28717957901567.30265312743.562751935218.3644661951
24.81014799652-2.89254452166-2.197942425759.333728296994.359420628364.71035713129-0.1251897451040.145799329407-0.3575103815580.1642754048140.0609271257903-0.4082712164430.3398010116910.3713639372090.06267329582530.3683099634050.0745106033929-0.04192186560170.5559646988830.08418177239720.40117948835184.535824159731.038856459616.8840218391
34.305400454571.089096059930.293579217424.15111147551.107763931023.80274508709-0.144103277305-0.724191700997-0.0006830676128670.7080159782680.041753565150.287841458633-0.02328226170970.1364231788260.08331012420270.471848016570.1061371110970.04381628725670.5103968195620.1140852167260.36317145399364.107867027444.27806699231.4775270285
42.65369474088-3.06667093844-3.018331882639.074941924476.845100780365.488681918410.0753182976179-0.9385145093660.4956287111470.679159596814-0.2594076265370.263249582573-0.507381877597-0.07775950712420.09501112652330.8047550293120.03948151121210.06274959501390.5567896857830.09299604675210.53414922352864.611527371755.664263362739.7043463281
51.735652039632.869024233143.474458497856.944324206543.711653119818.86968672593-0.200299706208-0.317098833666-0.02403804192330.2574136148360.08665772656191.09882750069-0.641527991761-1.206416213120.06492319087910.5414060367280.1810825360160.2013539760080.6849417858270.09996317581110.68441899756353.132987788849.811964623631.513152416
61.47594299230.589926782072-0.2911292010222.761976483961.265389876023.42009780775-0.2214994282930.273495511042-1.921250728510.0354749600877-0.07811758445850.5450929311220.7501652844740.2063730723940.2081291236430.538892900684-0.02123563102410.1323724025250.5684492828320.01740055687761.2313887129864.04823075419.394308760618.2018759486
71.71905650305-0.2910523810380.3920487989542.533204407020.7793833270510.382606400468-0.7279059213930.6383126506210.485124166233-0.6605301793190.8524620402770.4199625417080.7256441863750.2131979265710.004479565269881.33302137060.1362654318380.1501829413871.342803192740.4168047667541.2649530220170.80820446261.9867263129928.9342773317
80.946497053999-1.587357551330.8967213785864.45238266044-0.326996973855.8917105965-0.149920709578-0.432952540347-1.754039981310.696774037555-0.2255233937890.7218143882641.274181758180.2074878022880.343177432030.8478691771220.1134968958210.1724261295070.6477872841670.1732839834761.5069814274168.933218496110.903748757319.1083866528
96.40699994225-3.051156309551.349802759511.49833095305-0.9241551676942.529143178630.1551226971780.0578453576146-0.1237585131410.356551960940.3448308465951.24546028203-0.29720370785-0.699542539727-0.4231792879220.4681625564590.06759728739610.1262489484760.7338733422770.2422714054781.3632210341638.176452136961.009138269818.6830444802
101.614015813622.3386775042-3.323919027394.13666224399-5.766576046268.206710103290.3227220766330.431766652595-0.0384654020731.685740858950.4550029782661.53352951424-1.17467213617-0.709925046967-0.6887360159951.197891664930.2833015285930.2657262117531.521061060370.03679709196141.1864661226420.548349649791.321675049915.1026321138
119.253833309546.288928292123.167696322957.876870185586.817587136197.1756911425-0.748396413770.7534512786831.62598485914-1.662293630860.5479308141710.960311191763-0.05395202737740.0544088945770.3897899970631.21177146630.259404479045-0.01863829542511.225176816130.2250715708290.68593986935930.4152014344101.0387218986.22673746848
125.192867140793.59986976813-6.194533045278.29147003584-3.715965299818.959499269140.4170164497920.4606452856050.1692409677950.3534173192880.2264312656620.411058308599-0.990572560575-0.822141092454-0.6553712254710.9003592533520.329310159566-0.1138343486720.9841377714940.01650571470960.52896199530326.78329993191.50195243925.18717266857
134.37150173481-1.576298248121.251669085276.45415466178-3.20899325935.15471189164-0.09730718556720.360294071689-0.336357742283-0.1917614509760.3187876826310.571791609034-0.147252436578-0.00896426208077-0.209046819310.332421991538-0.0663202029131-0.04392119100030.4306355978590.02886522051110.50366560341657.33263835270.90624131299.92239730692
145.41999049282-0.451775183847-2.459675204321.677992802990.5093575955567.430083883360.233319986948-1.345759247440.5889589313240.532461990330.123376197589-0.0287475465263-0.8115724281891.16964725237-0.3516106644211.02893499234-0.0415552144607-0.1323586308180.9844185112930.02299698557160.53336412601141.545490334895.36108566389.76473758698
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 76 )CA1 - 761 - 76
22chain 'C' and (resid 77 through 186 )CA77 - 18677 - 186
33chain 'D' and (resid -25 through 48 )DF-25 - 481 - 60
44chain 'D' and (resid 49 through 61 )DF49 - 6161 - 73
55chain 'D' and (resid 62 through 74 )DF62 - 7474 - 86
66chain 'D' and (resid 75 through 130 )DF75 - 13087 - 135
77chain 'D' and (resid 131 through 142 )DF131 - 142136 - 145
88chain 'D' and (resid 143 through 188 )DF143 - 188146 - 186
99chain 'A' and (resid 1 through 128 )AH1 - 1281 - 114
1010chain 'A' and (resid 129 through 141 )AH129 - 141115 - 125
1111chain 'A' and (resid 142 through 154 )AH142 - 154126 - 136
1212chain 'A' and (resid 155 through 204 )AH155 - 203137 - 171
1313chain 'B' and (resid 1 through 133 )BI1 - 1331 - 120
1414chain 'B' and (resid 134 through 253 )BI134 - 253121 - 240

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