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- PDB-5swz: Crystal Structure of NP1-B17 TCR-H2Db-NP complex -

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Basic information

Entry
Database: PDB / ID: 5swz
TitleCrystal Structure of NP1-B17 TCR-H2Db-NP complex
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NP1-B17 TCR alpha chain
  • NP1-B17 TCR beta chain
  • influenza NP366 epitope
KeywordsIMMUNE SYSTEM / H2Db / influenza / NP366 / reversed docking / naive T cell / NP1-B17 TCR / TCR / T cell
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 / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / helical viral capsid / 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 / viral penetration into host nucleus / 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 / host cell / 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 / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / ribonucleoprotein complex / symbiont entry into host cell / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / host cell nucleus / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsGras, S. / Del Campo, C.M. / Farenc, C. / Josephs, T.M. / Rossjohn, J.
CitationJournal: Immunity / Year: 2016
Title: Reversed T Cell Receptor Docking on a Major Histocompatibility Class I Complex Limits Involvement in the Immune Response.
Authors: Gras, S. / Chadderton, J. / Del Campo, C.M. / Farenc, C. / Wiede, F. / Josephs, T.M. / Sng, X.Y. / Mirams, M. / Watson, K.A. / Tiganis, T. / Quinn, K.M. / Rossjohn, J. / La Gruta, N.L.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: influenza NP366 epitope
D: NP1-B17 TCR alpha chain
E: NP1-B17 TCR beta chain
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: influenza NP366 epitope
I: NP1-B17 TCR alpha chain
J: NP1-B17 TCR beta chain
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: influenza NP366 epitope
N: NP1-B17 TCR alpha chain
O: NP1-B17 TCR beta chain
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: influenza NP366 epitope
S: NP1-B17 TCR alpha chain
T: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,18731
Polymers384,56820
Non-polymers61811
Water9,584532
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: influenza NP366 epitope
D: NP1-B17 TCR alpha chain
E: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3578
Polymers96,1425
Non-polymers2153
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: influenza NP366 epitope
I: NP1-B17 TCR alpha chain
J: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1887
Polymers96,1425
Non-polymers462
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: H-2 class I histocompatibility antigen, D-B alpha chain
L: Beta-2-microglobulin
M: influenza NP366 epitope
N: NP1-B17 TCR alpha chain
O: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3578
Polymers96,1425
Non-polymers2153
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: H-2 class I histocompatibility antigen, D-B alpha chain
Q: Beta-2-microglobulin
R: influenza NP366 epitope
S: NP1-B17 TCR alpha chain
T: NP1-B17 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2848
Polymers96,1425
Non-polymers1423
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.231, 100.185, 469.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 16 molecules AFKPBGLQDINSEJOT

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32470.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#4: Protein
NP1-B17 TCR alpha chain


Mass: 23117.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein
NP1-B17 TCR beta chain


Mass: 27868.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide , 1 types, 4 molecules CHMR

#3: Protein/peptide
influenza NP366 epitope


Mass: 1026.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS

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Non-polymers , 3 types, 543 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.49 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 17% 3350, 0.2 KNaTartrate, 0.1 BTP 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→38.8 Å / Biso Wilson estimate: 66.83 Å2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 2.208 / Num. measured all: 272722 / Num. unique all: 18435 / CC1/2: 0.613 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Rsym value: 0.047 / Net I/σ(I) obs: 2 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUU, 1KGC

4huu

1kgc


Resolution: 2.65→38.8 Å / Cor.coef. Fo:Fc: 0.9015 / Cor.coef. Fo:Fc free: 0.8738 / SU R Cruickshank DPI: 0.711 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.701 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 6523 5.12 %RANDOM
Rwork0.2257 ---
obs0.2269 127456 99.98 %-
Displacement parametersBiso mean: 72.61 Å2
Baniso -1Baniso -2Baniso -3
1--6.0916 Å20 Å20 Å2
2---5.9491 Å20 Å2
3---12.0408 Å2
Refine analyzeLuzzati coordinate error obs: 0.482 Å
Refinement stepCycle: LAST / Resolution: 2.65→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26494 0 31 575 27100
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00727272HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9537068HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes749HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3917HARMONIC5
X-RAY DIFFRACTIONt_it27272HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion21.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact27932SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3181 472 5.07 %
Rwork0.2952 8846 -
all0.2964 9318 -
obs--99.98 %
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)
11.87340.0392-1.51340.3840.09452.57640.0188-0.01640.14750.05130.013-0.13540.04860.2911-0.0317-0.07920.03960.00810.00320.12-0.082763.8336-3.3582-26.5018
22.64990.11720.00070.3632-0.30873.11860.01550.1476-0.0533-0.10590.01450.0579-0.0001-0.0111-0.030.00780.13720.01060.09940.1273-0.13952.392-3.5179-42.5299
31.4198-0.2268-1.14720.47720.05953.2299-0.0343-0.0630.2571-0.02110.07770.0597-0.0851-0.0773-0.0433-0.06620.002-0.0026-0.0370.12620.06117.3678-6.594917.6841
41.0713-0.3324-1.00120.8671-1.31594.1351-0.0155-0.14390.09850.04670.06830.0067-0.14230.1259-0.0528-0.0778-0.0404-0.0347-0.0210.0366-0.12436.6774-8.708624.3642
50.0162-0.91060.72032.4644-2.29472.0406-0.05920.0361-0.08660.0297-0.10820.02430.26360.28130.1674-0.06650.14920.14940.21650.1447-0.19124.3263-47.7013-92.0446
60.9751-1.1724-0.93560.91840.33442.70670.0197-0.13770.09380.1707-0.0235-0.1022-0.00680.10760.0039-0.01240.14790.15190.24220.1516-0.164923.795-36.2468-75.9837
70.17570.02560.7811.3625-1.31122.76580.0314-0.09610.129-0.2062-0.04-0.0362-0.08170.0170.0086-0.04770.06410.1520.10490.0741-0.005126.5408-1.5613-135.191
82.01050.1901-2.42750.91920.55255.7657-0.0108-0.1518-0.1768-0.42250.159-0.082-0.2728-0.0271-0.1481-0.01760.10480.1275-0.03640.0181-0.232930.5188-19.6554-142.44
90.18390.21870.71260.8388-0.66372.9013-0.0455-0.1157-0.1291-0.25110.070.2420.1224-0.236-0.0245-0.02930.0352-0.03560.0122-0.0619-0.0539-13.0611-25.7993-118.511
101.44421.7329-0.92581.753-0.03872.8385-0.0140.07780.1116-0.1466-0.05610.1131-0.08230.00250.0701-0.01850.1071-0.07730.0352-0.0646-0.0834-2.3513-13.3744-129.717
110.5286-0.71650.65850.0356-0.62873.99520.0127-0.2478-0.0579-0.1540.0534-0.0631-0.04820.1428-0.066-0.0674-0.14730.03940.1945-0.0069-0.110511.8993-12.9284-60.826
120.1897-0.287-0.3340.26710.16655.18130.0162-0.1328-0.0268-0.05060.0348-0.06410.13420.0729-0.051-0.1693-0.00870.02670.15510.0274-0.0946-4.4496-24.7064-60.7412
130.7278-0.22320.12151.30660.75312.5656-0.0173-0.13920.2490.1209-0.02580.0358-0.11360.17470.0431-0.1005-0.07250.099-0.04380.0140.124439.827734.8247-5.2079
141.09410.2374-1.34110.0008-0.21321.8381-0.001-0.16130.05390.12290.01910.058-0.0246-0.117-0.0181-0.0549-0.09240.13110.16770.0145-0.042728.272523.172510.7948
150.5325-0.1149-1.15430.62460.63724.24510.02850.1283-0.1186-0.1351-0.0340.10430.0707-0.08520.0055-0.12250.0658-0.03310.07320.1090.075130.080110.2606-59.5446
160.3928-0.0081-1.32940.19290.42566.35710.11210.08930.0276-0.0771-0.1350.0534-0.22080.05460.0229-0.00370.14740.0191-0.05420.145-0.062442.545926.2469-57.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|277 }A1 - 277
2X-RAY DIFFRACTION2{ B|1 - B|99 }B1 - 99
3X-RAY DIFFRACTION3{ D|1 - D|216 }D1 - 216
4X-RAY DIFFRACTION4{ E|3 - E|255 }E3 - 255
5X-RAY DIFFRACTION5{ F|1 - F|277 }F1 - 277
6X-RAY DIFFRACTION6{ G|1 - G|99 }G1 - 99
7X-RAY DIFFRACTION7{ I|1 - I|205 }I1 - 205
8X-RAY DIFFRACTION8{ J|3 - J|255 }J3 - 255
9X-RAY DIFFRACTION9{ K|1 - K|277 }K1 - 277
10X-RAY DIFFRACTION10{ L|1 - L|99 }L1 - 99
11X-RAY DIFFRACTION11{ N|1 - N|217 }N1 - 217
12X-RAY DIFFRACTION12{ O|3 - O|256 }O3 - 256
13X-RAY DIFFRACTION13{ P|1 - P|271 }P1 - 271
14X-RAY DIFFRACTION14{ Q|2 - Q|99 }Q2 - 99
15X-RAY DIFFRACTION15{ S|1 - S|217 }S1 - 217
16X-RAY DIFFRACTION16{ T|3 - T|254 }T3 - 254

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