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- PDB-6hby: HLA class II peptide flanking residues tune the immunogenicity of... -

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Basic information

Entry
Database: PDB / ID: 6hby
TitleHLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope
Components
  • (HLA class II histocompatibility antigen, DR alpha ...) x 2
  • ARRPPLAELAALNLSGSRL 5T4 tumour epitope
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / HLA Class II / MHC II / Human / 5T4 tumor epitope
Function / homology
Function and homology information


mesenchymal cell migration / dendrite arborization / 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 ...mesenchymal cell migration / dendrite arborization / 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 / olfactory learning / 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 chemotaxis / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of synapse assembly / intermediate filament / T-helper 1 type immune response / synaptic transmission, GABAergic / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / axon terminus / MHC class II antigen presentation / trans-Golgi network membrane / protein localization to plasma membrane / lumenal side of endoplasmic reticulum membrane / cell chemotaxis / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / negative regulation of canonical Wnt signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / 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 / positive regulation of protein phosphorylation / early endosome membrane / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cell adhesion / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / negative regulation of cell population proliferation / dendrite / positive regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain ...: / Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Trophoblast glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMacLachlan, B. / Rizkallah, P.J. / Sewell, A.K. / Cole, D.K. / Godkin, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope.
Authors: MacLachlan, B.J. / Dolton, G. / Papakyriakou, A. / Greenshields-Watson, A. / Mason, G.H. / Schauenburg, A. / Besneux, M. / Szomolay, B. / Elliott, T. / Sewell, A.K. / Gallimore, A. / ...Authors: MacLachlan, B.J. / Dolton, G. / Papakyriakou, A. / Greenshields-Watson, A. / Mason, G.H. / Schauenburg, A. / Besneux, M. / Szomolay, B. / Elliott, T. / Sewell, A.K. / Gallimore, A. / Rizkallah, P. / Cole, D.K. / Godkin, A.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,16636
Polymers90,1396
Non-polymers2,02730
Water5,152286
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,22622
Polymers44,9483
Non-polymers1,27819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,94014
Polymers45,1923
Non-polymers74911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.960, 121.290, 68.960
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAA3 - 1791 - 177
21GLUGLUGLUGLUDD3 - 1792 - 178
12GLYGLYARGARGBB1 - 1892 - 190
22GLYGLYARGARGEE1 - 1892 - 190
13ALAALALEULEUCC2 - 201 - 19
23ALAALALEULEUFF2 - 201 - 19

NCS ensembles :
ID
1
2
3

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Components

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HLA class II histocompatibility antigen, DR alpha ... , 2 types, 2 molecules AD

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


Mass: 20727.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#4: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 20971.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903

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Protein / Protein/peptide , 2 types, 4 molecules BECF

#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 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide ARRPPLAELAALNLSGSRL 5T4 tumour epitope


Mass: 2008.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13641*PLUS

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Non-polymers , 3 types, 316 molecules

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


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 7.5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→60.64 Å / Num. obs: 64792 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.144 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4807 / CC1/2: 0.589 / Rrim(I) all: 1.295 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→60.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.678 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 3165 4.9 %RANDOM
Rwork0.19307 ---
obs0.19539 61597 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.763 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å2-0.14 Å2
2--0.4 Å2-0 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 1.95→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 125 286 6762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196648
X-RAY DIFFRACTIONr_bond_other_d0.0070.026179
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.958995
X-RAY DIFFRACTIONr_angle_other_deg1.4314182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9723.391345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.267151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5951558
X-RAY DIFFRACTIONr_chiral_restr0.1090.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217420
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021614
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3352.7393112
X-RAY DIFFRACTIONr_mcbond_other2.3242.7373111
X-RAY DIFFRACTIONr_mcangle_it3.4824.0863883
X-RAY DIFFRACTIONr_mcangle_other3.4824.0893884
X-RAY DIFFRACTIONr_scbond_it3.0743.1493536
X-RAY DIFFRACTIONr_scbond_other3.0263.1223516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6034.5315083
X-RAY DIFFRACTIONr_long_range_B_refined7.08322.3337012
X-RAY DIFFRACTIONr_long_range_B_other7.04822.1866959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A198740.08
12D198740.08
21B208580.09
22E208580.09
31C14100.19
32F14100.19
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 247 -
Rwork0.325 4557 -
obs--99.85 %
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)
13.0547-1.72340.79771.9013-1.06532.7772-0.0294-0.12320.21490.1319-0.0057-0.1296-0.2741-0.04820.03510.1651-0.0044-0.01710.0131-0.00690.017548.718411.6656100.3156
22.1161-0.0468-0.05973.7641-2.42884.1410.04490.41670.2446-0.3288-0.2023-0.3868-0.2070.47470.15740.2333-0.00850.02610.15410.04440.081860.459413.749280.051
31.1018-0.1931-0.60591.6648-0.89742.4937-0.0005-0.0071-0.26440.01640.00330.1483-0.0854-0.1301-0.00270.15460.0412-0.03230.01940.00050.083842.1756-0.096102.2921
41.4049-1.2973-1.6761.88571.73346.35610.12580.4416-0.1436-0.3456-0.24450.1767-0.2088-0.81410.11870.32290.0575-0.01920.2259-0.02610.021142.057110.141863.4596
511.3139-9.31714.286910.3463-6.2155.1877-0.6211-0.43921.41121.0782-0.0655-1.4868-0.8544-0.14810.68660.3397-0.0054-0.14740.28020.07250.248642.826811.2609108.7211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 78
2X-RAY DIFFRACTION2A89 - 180
3X-RAY DIFFRACTION3B5 - 92
4X-RAY DIFFRACTION4B93 - 190
5X-RAY DIFFRACTION5C2 - 20

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