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- PDB-2nw3: Crystal structure of HLA-B*3508 presenting EBV peptide EPLPQGQLTA... -

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Basic information

Entry
Database: PDB / ID: 2nw3
TitleCrystal structure of HLA-B*3508 presenting EBV peptide EPLPQGQLTAY at 1.7A
Components
  • Beta-2-microglobulin
  • EBV peptide EPLPQGQLTAY
  • HLA class I histocompatibility antigen, B-35 alpha chain
KeywordsIMMUNE SYSTEM / MHC / HLA-B*3508
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTynan, F.E. / Reid, H.H. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2007
Title: A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule
Authors: Tynan, F.E. / Reid, H.H. / Kjer-Nielsen, L. / Miles, J.J. / Wilce, M.C. / Kostenko, L. / Borg, N.A. / Williamson, N.A. / Beddoe, T. / Purcell, A.W. / Burrows, S.R. / McCluskey, J. / Rossjohn, J.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: EBV peptide EPLPQGQLTAY


Theoretical massNumber of molelcules
Total (without water)44,9493
Polymers44,9493
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-21 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.832, 81.661, 110.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31984.281 Da / Num. of mol.: 1 / Fragment: residues 1-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide EBV peptide EPLPQGQLTAY


Mass: 1216.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M Ammonium acetate, 0.1M Cacodylate (pH7.7), 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.7→65.653 Å / Num. obs: 50052 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.70.4041.92560069790.40494.9
1.79-1.93.80.2413.12541967280.24196
1.9-2.033.80.1415.22410763610.14196.8
2.03-2.193.80.0937.92276259920.09397.8
2.19-2.43.80.06710.72139156210.06798.5
2.4-2.693.80.05113.71930550680.05199.1
2.69-3.13.80.03717.41742845730.03799.8
3.1-3.83.80.029191479539040.029100
3.8-5.383.70.02621.51154530820.026100
5.38-22.213.60.02915.7632517440.02997.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZSD

1zsd


Resolution: 1.7→22.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.313 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2520 5 %RANDOM
Rwork0.201 ---
obs0.203 49994 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.661 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 0 423 3637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213268
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9364445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20622.802182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13115537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1031537
X-RAY DIFFRACTIONr_chiral_restr0.0990.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022605
X-RAY DIFFRACTIONr_nbd_refined0.2110.21597
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2373
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.229
X-RAY DIFFRACTIONr_mcbond_it1.99131983
X-RAY DIFFRACTIONr_mcangle_it2.84353103
X-RAY DIFFRACTIONr_scbond_it4.20171505
X-RAY DIFFRACTIONr_scangle_it6.072101336
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 170 -
Rwork0.397 3354 -
obs-3524 94.43 %

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