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- PDB-6r0e: Structure of F11TCR in complex with DR1 MHC Class II presenting P... -

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Basic information

Entry
Database: PDB / ID: 6r0e
TitleStructure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • F11-TCR Alpha Chain
  • F11-TCR Beta Chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / FLU / MHC Class II / Human / DR1 / HLA-DR1 / 3D
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / negative regulation of inflammatory response to antigenic stimulus / peptide antigen assembly with MHC class II protein complex / clathrin-coated endocytic vesicle membrane / MHC class II protein complex / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / structural constituent of cytoskeleton / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / lysosome / positive regulation of viral entry into host cell / host cell surface receptor binding / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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
DI(HYDROXYETHYL)ETHER / HLA class II histocompatibility antigen, DR alpha chain / Hemagglutinin / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRizkallah, P.J. / Greenshields-Watson, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell Rep / Year: 2020
Title: CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features.
Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / ...Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / Geary, J. / Chen, Y. / Lauder, S.N. / Smart, K. / Vijaykrishna, D. / Grau, M.L. / Shugay, M. / Andrews, R. / Dolton, G. / Rizkallah, P.J. / Gallimore, A.M. / Sewell, A.K. / Godkin, A.J. / Cole, D.K.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen, DRB1-1 beta chain
CCC: Hemagglutinin
DDD: F11-TCR Alpha Chain
EEE: F11-TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,33314
Polymers94,6525
Non-polymers6819
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint-70 kcal/mol
Surface area36640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.280, 184.900, 50.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AAABBB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21287.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR1


Mass: 22211.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229

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Protein/peptide , 1 types, 1 molecules CCC

#3: Protein/peptide Hemagglutinin


Mass: 1506.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03435

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Protein , 2 types, 2 molecules DDDEEE

#4: Protein F11-TCR Alpha Chain


Mass: 22438.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein F11-TCR Beta Chain


Mass: 27208.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 317 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M Na Cacodylate, 0.2 M NH4 SO4, 15 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.91→92.46 Å / Num. obs: 96543 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 14.1
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.26 / Num. unique obs: 7001 / Rpim(I) all: 0.491 / Rrim(I) all: 1.354 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYT

1fyt


Resolution: 1.91→92.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.21 / SU B: 7.516 / SU ML: 0.105 / Average fsc free: 0.903 / Average fsc work: 0.9121 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2332 4763 4.938 %
Rwork0.2055 91698 -
all0.207 --
obs-96461 99.905 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.331 Å2-0 Å2-0 Å2
2---0.679 Å20 Å2
3---1.009 Å2
Refinement stepCycle: LAST / Resolution: 1.91→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6567 0 43 308 6918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176049
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.659288
X-RAY DIFFRACTIONr_angle_other_deg1.3161.57414041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.6565.42858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26422.356365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.772151066
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.6671510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0131543
X-RAY DIFFRACTIONr_chiral_restr0.0770.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028513
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021501
X-RAY DIFFRACTIONr_nbd_refined0.2010.21098
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25783
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23129
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2320
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.220
X-RAY DIFFRACTIONr_nbd_other0.2150.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.221
X-RAY DIFFRACTIONr_mcbond_it1.6132.5463317
X-RAY DIFFRACTIONr_mcbond_other1.6132.5453316
X-RAY DIFFRACTIONr_mcangle_it2.5563.8034148
X-RAY DIFFRACTIONr_mcangle_other2.5553.8044149
X-RAY DIFFRACTIONr_scbond_it2.2192.8033509
X-RAY DIFFRACTIONr_scbond_other2.2192.8053510
X-RAY DIFFRACTIONr_scangle_it3.3824.0885139
X-RAY DIFFRACTIONr_scangle_other3.3824.0895140
X-RAY DIFFRACTIONr_lrange_it6.54229.5177202
X-RAY DIFFRACTIONr_lrange_other6.54329.5267203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.91-1.960.3853330.33566650.33870020.7580.76599.94290.331
1.96-2.0130.3043440.28965650.2969100.8220.84299.98550.279
2.013-2.0720.2733290.26163280.26266660.8660.87299.8650.249
2.072-2.1350.2733210.23561740.23764950.8960.8951000.221
2.135-2.2050.2713180.22259830.22563020.8980.91199.98410.206
2.205-2.2830.2513130.21958400.2261600.9140.92499.88640.203
2.283-2.3690.2423010.20955720.2158740.9190.92499.9830.19
2.369-2.4650.2372810.18953560.19156370.9250.9431000.171
2.465-2.5750.2312790.18851810.1954620.9280.94699.96340.172
2.575-2.7010.2612560.19749920.252490.9220.9499.98090.181
2.701-2.8470.242500.247300.20249800.9370.9441000.187
2.847-3.0190.2362350.19344860.19547300.9340.94499.80970.187
3.019-3.2270.2132120.18942390.1944530.9450.94999.95510.19
3.227-3.4850.2192030.20139450.20241510.9440.94599.92770.207
3.485-3.8180.2271850.20436610.20538500.9380.94499.89610.217
3.818-4.2670.2321510.1933530.19235130.9390.9599.74380.213
4.267-4.9260.1941650.17529260.17630910.9590.9641000.208
4.926-6.0280.2211310.21125170.21226620.9440.95199.47410.241
6.028-8.5070.2531140.2319980.23121150.9340.9499.85820.264
8.507-92.450.159420.20211870.212500.970.96398.320.239
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)
11.4346-0.5039-0.18763.49990.28521.26930.04970.1285-0.2938-0.2448-0.15250.2461-0.07-0.21820.10290.09590.1512-0.07390.3045-0.05340.2952-45.91834.3803-28.0801
24.91393.6513-3.57393.1443-2.91585.78990.2018-0.4572-0.1030.3463-0.24920.45670.1551-0.40050.04740.30180.16240.16750.5671-0.08610.7613-66.699939.6959-12.2557
37.06580.63440.15270.1010.03030.01450.06790.41880.0312-0.0515-0.0602-0.1158-0.0243-0.076-0.00760.24210.06070.00330.7868-0.03170.7024-84.184622.5419-24.5455
41.2969-0.885-0.60771.80131.53872.5886-0.0151-0.06370.0523-0.0329-0.08110.1494-0.3609-0.27230.09620.15630.1209-0.02630.1571-0.0060.0815-20.118122.3323-23.8972
52.7382-0.1197-0.36796.06431.65073.1591-0.0762-0.1268-0.06380.45660.1553-0.27670.07730.1865-0.07910.03820.0131-0.01350.0655-0.00740.043412.37957.276-28.4647
61.52390.0919-1.21062.29750.53975.0527-0.0531-0.0768-0.02760.22040.1498-0.2287-0.15340.1732-0.09680.0505-0.0023-0.0270.0389-0.00070.032610.110821.9877-19.7474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 82
2X-RAY DIFFRACTION1ALLBBB0 - 93
3X-RAY DIFFRACTION1ALLCCC1 - 13
4X-RAY DIFFRACTION2ALLAAA83 - 180
5X-RAY DIFFRACTION3ALLBBB94 - 189
6X-RAY DIFFRACTION4ALLDDD0 - 111
7X-RAY DIFFRACTION4ALLEEE0 - 110
8X-RAY DIFFRACTION5ALLDDD112 - 201
9X-RAY DIFFRACTION6ALLEEE111 - 239

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