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- PDB-4qrq: Crystal Structure of HLA B*0801 in complex with HSKKKCDEL -

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Basic information

Entry
Database: PDB / ID: 4qrq
TitleCrystal Structure of HLA B*0801 in complex with HSKKKCDEL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-8 alpha chain
  • NS3-4A protein
KeywordsIMMUNE SYSTEM / HLA B*0801 / human hepatitis C virus / TCR / T cell
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 / symbiont-mediated transformation of host cell / protection from natural killer cell mediated cytotoxicity / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated transformation of host cell / protection from natural killer cell mediated cytotoxicity / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / serine-type peptidase activity / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of T cell mediated cytotoxicity / secretory granule membrane / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral capsid / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / ribonucleoside triphosphate phosphatase activity / DAP12 signaling / late endosome membrane / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / RNA helicase activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / lysosomal membrane / focal adhesion / fusion of virus membrane with host endosome membrane / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / proteolysis / : / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...: / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / 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 / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 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 / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGras, S. / Berry, R. / Lucet, I.S. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2014
Title: An Extensive Antigenic Footprint Underpins Immunodominant TCR Adaptability against a Hypervariable Viral Determinant.
Authors: Nivarthi, U.K. / Gras, S. / Kjer-Nielsen, L. / Berry, R. / Lucet, I.S. / Miles, J.J. / Tracy, S.L. / Purcell, A.W. / Bowden, D.S. / Hellard, M. / Rossjohn, J. / McCluskey, J. / Bharadwaj, M.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 16, 2020Group: Database references / Structure summary / Category: struct_keywords / struct_ref_seq_dif / Item: _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: NS3-4A protein


Theoretical massNumber of molelcules
Total (without water)44,8993
Polymers44,8993
Non-polymers00
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-17 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.836, 81.511, 110.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 31927.977 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: P30460, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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 NS3-4A protein


Mass: 1091.281 Da / Num. of mol.: 1 / Fragment: unp residues 369-377 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: X2G898
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 51.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1 tri-Na citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 51051 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.944 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.45
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.90.5513.92199.9
1.9-20.3386.54198.8
2-2.10.2588.46199.5
2.1-2.20.18211.141100
2.2-2.30.17212.58198.7
2.3-2.50.12815.061100
2.5-2.60.10217.771100
2.6-2.70.10418.81100
2.7-30.07222.911100
3-40.04734.27199.9
4-50.03346.191100
5-60.03543.161100
6-100.03443.051100
100.0348.02184.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1m05

1m05


Resolution: 1.7→24.394 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 19.96 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2092 2590 5.07 %
Rwork0.1814 --
obs0.1829 51051 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8348 Å2
Baniso -1Baniso -2Baniso -3
1--0.1778 Å2-0 Å20 Å2
2---2.5496 Å2-0 Å2
3---2.7274 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 0 590 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073308
X-RAY DIFFRACTIONf_angle_d1.0984497
X-RAY DIFFRACTIONf_dihedral_angle_d14.9871243
X-RAY DIFFRACTIONf_chiral_restr0.082455
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.73270.26861350.20982384X-RAY DIFFRACTION91
1.7327-1.76810.24151320.21132626X-RAY DIFFRACTION97
1.7681-1.80650.27441510.21622656X-RAY DIFFRACTION100
1.8065-1.84850.22981460.20242672X-RAY DIFFRACTION100
1.8485-1.89480.20741490.19012669X-RAY DIFFRACTION100
1.8948-1.9460.23441430.19442692X-RAY DIFFRACTION100
1.946-2.00320.26761360.20572669X-RAY DIFFRACTION100
2.0032-2.06780.22791360.18652690X-RAY DIFFRACTION100
2.0678-2.14170.23821340.18662725X-RAY DIFFRACTION100
2.1417-2.22740.22471610.18262657X-RAY DIFFRACTION100
2.2274-2.32870.21521310.18042727X-RAY DIFFRACTION100
2.3287-2.45130.22091620.18912679X-RAY DIFFRACTION100
2.4513-2.60480.24311410.18992712X-RAY DIFFRACTION100
2.6048-2.80560.22871320.18782740X-RAY DIFFRACTION100
2.8056-3.08750.21061620.18482706X-RAY DIFFRACTION100
3.0875-3.53310.19321540.1692744X-RAY DIFFRACTION100
3.5331-4.44690.15891570.15742776X-RAY DIFFRACTION100
4.4469-24.39650.1771280.17332937X-RAY DIFFRACTION100

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