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- PDB-5eo0: Crystal Structure of HLA-B0702-RFL9 -

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Basic information

Entry
Database: PDB / ID: 5eo0
TitleCrystal Structure of HLA-B0702-RFL9
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • RFL9 peptide
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA B*0702 / HIV / immune escape
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 / : ...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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / SH3 domain binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / virion component / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / 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 protein binding / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell perinuclear region of cytoplasm / : / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / innate immune response / focal adhesion / Neutrophil degranulation / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 / Protein Nef / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsJosephs, T.M. / Gras, S. / Rossjohn, J.
CitationJournal: J Immunol. / Year: 2016
Title: HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection.
Authors: Du, V.Y. / Bansal, A. / Carlson, J. / Salazar-Gonzalez, J.F. / Salazar, M.G. / Ladell, K. / Gras, S. / Josephs, T.M. / Heath, S.L. / Price, D.A. / Rossjohn, J. / Hunter, E. / Goepfert, P.A.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
C: RFL9 peptide


Theoretical massNumber of molelcules
Total (without water)44,8643
Polymers44,8643
Non-polymers00
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-15 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.837, 81.980, 110.768
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-7 alpha chain / MHC class I antigen B*7


Mass: 31962.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide RFL9 peptide


Mass: 1022.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) / References: UniProt: P12478*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 4000 and 0.1 M Ammonium acetate, 0.1 M Na-cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.7→37.37 Å / Num. all: 51552 / Num. obs: 51552 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 12.33 Å2 / Rmerge(I) obs: 0.647 / Rpim(I) all: 0.261 / Rrim(I) all: 0.699 / Rsym value: 0.647 / Net I/σ(I): 6.6 / Num. measured all: 362268
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym value% possible all
1.7-1.797.17.3451.95280374110.0360.086100
5.38-37.376.60.08614.31190618000.0380.09599.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.37 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 2562 5.07 %
Rwork0.1659 48002 -
obs0.1682 50564 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.65 Å2 / Biso mean: 16.1487 Å2 / Biso min: 0.99 Å2
Refinement stepCycle: final / Resolution: 1.7→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 488 3643
Biso mean---26.61 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153553
X-RAY DIFFRACTIONf_angle_d1.5354884
X-RAY DIFFRACTIONf_chiral_restr0.079498
X-RAY DIFFRACTIONf_plane_restr0.008658
X-RAY DIFFRACTIONf_dihedral_angle_d14.4681424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73270.26811390.225126432782100
1.7327-1.76810.26611530.21312690284399
1.7681-1.80650.24131540.20332641279599
1.8065-1.84850.25371420.19412666280899
1.8485-1.89480.25441480.19062673282199
1.8948-1.9460.24611530.17762687284099
1.946-2.00330.27571450.17732647279299
2.0033-2.06790.2081420.16512671281399
2.0679-2.14180.22221250.17212698282399
2.1418-2.22760.21521440.16392646279098
2.2276-2.3290.21591540.15762657281198
2.329-2.45180.20791210.15982683280498
2.4518-2.60540.20391300.16682670280097
2.6054-2.80650.21121240.17412673279797
2.8065-3.08890.23491490.17012647279697
3.0889-3.53570.17551430.15352655279896
3.5357-4.4540.19451410.13772660280195
4.454-45.90930.16821550.15132695285092

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