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- PDB-6qza: HLA-DR1 with GMF Influenza PB1 Peptide -

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Basic information

Entry
Database: PDB / ID: 6qza
TitleHLA-DR1 with GMF Influenza PB1 Peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
  • PB1-410-422-GMF-Peptide
KeywordsIMMUNE SYSTEM / HLA-DR1 / CD4 / T-cell / Influenza / Polymerase Basic-1 / Conserved / Epitopes
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 / positive regulation of T cell mediated immune response to tumor cell / 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 ...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 / positive regulation of T cell mediated immune response to tumor cell / 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 memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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
HLA class II histocompatibility antigen, DR alpha chain / 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: 3.09 Å
AuthorsGreenshields-Watson, A. / Rizkallah, P.J.
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 11, 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.identifier_ORCID / _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

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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: PB1-410-422-GMF-Peptide
DDD: HLA class II histocompatibility antigen, DR alpha chain
EEE: HLA class II histocompatibility antigen, DRB1-1 beta chain
FFF: PB1-410-422-GMF-Peptide


Theoretical massNumber of molelcules
Total (without water)91,2576
Polymers91,2576
Non-polymers00
Water00
1
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen, DRB1-1 beta chain
CCC: PB1-410-422-GMF-Peptide


Theoretical massNumber of molelcules
Total (without water)45,6293
Polymers45,6293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-44 kcal/mol
Surface area18240 Å2
MethodPISA
2
DDD: HLA class II histocompatibility antigen, DR alpha chain
EEE: HLA class II histocompatibility antigen, DRB1-1 beta chain
FFF: PB1-410-422-GMF-Peptide


Theoretical massNumber of molelcules
Total (without water)45,6293
Polymers45,6293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-41 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.017, 184.017, 87.285
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA DDD
22Chains BBB EEE
33Chains CCC FFF

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 21287.102 Da / Num. of mol.: 2
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.: 2
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
#3: Protein/peptide PB1-410-422-GMF-Peptide


Mass: 2129.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus

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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: 4.67 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: Seeded with DR1-QAR crystals. 0.2M LiCl, 20% PEG 6K, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97265 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97265 Å / Relative weight: 1
ReflectionResolution: 3.086→92.02 Å / Num. obs: 31506 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.06 / Rrim(I) all: 0.201 / Net I/σ(I): 10.3
Reflection shellResolution: 3.086→3.17 Å / Redundancy: 10.9 % / Rmerge(I) obs: 3.078 / Num. unique obs: 2293 / Rpim(I) all: 0.979 / Rrim(I) all: 3.231 / % possible all: 100

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Processing

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

1dlh


Resolution: 3.09→92.008 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 35.184 / SU ML: 0.256 / Cross valid method: FREE R-VALUE / ESU R: 0.621 / ESU R Free: 0.322
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2259 1532 4.875 %
Rwork0.1834 --
all0.185 --
obs-31427 99.557 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.326 Å2
Baniso -1Baniso -2Baniso -3
1--0.148 Å2-0.074 Å20 Å2
2---0.148 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 3.09→92.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 0 0 6148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126318
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6428600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7255747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73521.832382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.243151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6461550
X-RAY DIFFRACTIONr_chiral_restr0.1210.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024994
X-RAY DIFFRACTIONr_nbd_refined0.2380.22523
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2152
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.21
X-RAY DIFFRACTIONr_mcbond_it1.6973.2733012
X-RAY DIFFRACTIONr_mcangle_it2.9324.9013751
X-RAY DIFFRACTIONr_scbond_it2.3843.4533305
X-RAY DIFFRACTIONr_scangle_it3.9635.1014849
X-RAY DIFFRACTIONr_lrange_it6.2543.0759096
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.055344
X-RAY DIFFRACTIONr_ncsr_local_group_20.1140.055411
X-RAY DIFFRACTIONr_ncsr_local_group_30.1710.05214
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
3.086-3.1660.351960.33321140.33422950.7760.78496.29630.33
3.166-3.2530.3691250.29221540.29722800.7660.81399.95610.282
3.253-3.3470.2981050.25720770.25921850.8620.87699.86270.243
3.347-3.450.2871070.24420130.24621250.8760.89599.76470.229
3.45-3.5630.229730.22119710.22120450.9170.92199.95110.206
3.563-3.6870.2181060.20618880.20619950.9330.92999.94990.191
3.687-3.8260.284970.20718370.2119390.9020.92899.74210.192
3.826-3.9820.2261100.18317600.18518760.9340.94499.68020.171
3.982-4.1590.201780.16617090.16817920.9490.95599.7210.155
4.159-4.3620.186900.13515950.13716880.9590.97299.82230.129
4.362-4.5970.156730.12215540.12316320.9710.97899.69360.118
4.597-4.8750.144650.11414830.11515500.9760.98199.8710.112
4.875-5.2110.123750.11313620.11314390.9830.98299.8610.111
5.211-5.6260.193620.13912970.14113610.9570.97299.85310.138
5.626-6.1610.225730.18711890.18912640.9460.95699.84180.187
6.161-6.8850.182500.210810.19911320.9470.9599.91170.2
6.885-7.9420.258490.1849660.18710160.9280.95299.90160.19
7.942-9.7090.199350.168350.1628710.9560.96699.88520.172
9.709-13.6550.237450.1826250.1856700.9470.961000.195
13.655-92.0080.601180.2973850.3074100.7640.89198.29270.372
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)
15.94681.51760.0452.9021.13823.7994-0.1079-0.25440.98570.138-0.030.6349-0.6390.20320.13790.2679-0.1852-0.03870.24840.04310.2521-57.57171.05481.4305
28.5151.49356.24370.80170.95738.0730.28150.8281-0.5513-0.14870.1026-0.02230.44380.0212-0.38410.189-0.1105-0.05510.4080.00930.1013-64.36554.6801-19.3176
38.85935.14680.626312.65240.96153.4150.19630.3747-0.16280.04240.0260.03080.6979-0.3724-0.22240.1645-0.1057-0.07350.30820.12460.0725-83.751243.8388-7.0437
46.37911.85071.19152.60740.51166.05381.1286-0.4303-1.69370.2761-0.1107-0.55011.12770.0602-1.01790.5483-0.1995-0.57240.36340.18090.7527-60.367535.875810.0488
53.2550.32733.02812.37811.793711.24030.5186-0.3717-0.30740.36790.0684-0.30230.17740.5365-0.5870.2985-0.2848-0.21380.64460.10370.4331-43.07850.08126.0668
64.9911.26250.665612.45160.90425.32630.2047-1.20730.77810.8491-0.19460.5364-0.7459-0.9609-0.01010.4272-0.16440.1110.9764-0.12710.1586-60.969567.801231.4435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 82
2X-RAY DIFFRACTION1ALLBBB1 - 93
3X-RAY DIFFRACTION1ALLCCC2 - 16
4X-RAY DIFFRACTION2ALLAAA83 - 181
5X-RAY DIFFRACTION3ALLBBB94 - 190
6X-RAY DIFFRACTION4ALLDDD3 - 82
7X-RAY DIFFRACTION4ALLEEE3 - 93
8X-RAY DIFFRACTION4ALLFFF3 - 16
9X-RAY DIFFRACTION5ALLDDD83 - 181
10X-RAY DIFFRACTION6ALLEEE94 - 190

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