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- PDB-4qru: Crystal Structure of HLA B*0801 in complex with ELR_MYM, ELRRKMMYM -

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Basic information

Entry
Database: PDB / ID: 4qru
TitleCrystal Structure of HLA B*0801 in complex with ELR_MYM, ELRRKMMYM
Components
  • 55 kDa immediate-early protein 1
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-8 alpha chain
KeywordsIMMUNE SYSTEM / HLA B*0801 / CMV / TCR / T cell
Function / homology
Function and homology information


DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane ...DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / virus-mediated perturbation of host defense response / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / 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 / : ...Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / Immediate early protein IE1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 5 strain Towne
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGras, S. / Twist, K.-A. / Rossjohn, J.
CitationJournal: Sci Rep / Year: 2014
Title: Molecular imprint of exposure to naturally occurring genetic variants of human cytomegalovirus on the T cell repertoire.
Authors: Smith, C. / Gras, S. / Brennan, R.M. / Bird, N.L. / Valkenburg, S.A. / Twist, K.A. / Burrows, J.M. / Miles, J.J. / Chambers, D. / Bell, S. / Campbell, S. / Kedzierska, K. / Burrows, S.R. / ...Authors: Smith, C. / Gras, S. / Brennan, R.M. / Bird, N.L. / Valkenburg, S.A. / Twist, K.A. / Burrows, J.M. / Miles, J.J. / Chambers, D. / Bell, S. / Campbell, S. / Kedzierska, K. / Burrows, S.R. / Rossjohn, J. / Khanna, R.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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 / pdbx_entry_details / pdbx_modification_feature / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 55 kDa immediate-early protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0555
Polymers44,9373
Non-polymers1182
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-22 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 81.180, 109.810
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: 11748.160 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 55 kDa immediate-early protein 1 / IE1


Mass: 1260.615 Da / Num. of mol.: 1 / Fragment: unp residues 199-207 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 strain Towne / References: UniProt: P03169
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
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: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→27.921 Å / Num. all: 56374 / Num. obs: 56374 / % possible obs: 92.8 % / Redundancy: 6.6 % / Rsym value: 0.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.921 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 2805 4.98 %
Rwork0.1775 --
obs0.1787 56323 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9759 Å2-0 Å20 Å2
2---1.4991 Å2-0 Å2
3---3.475 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 8 579 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073494
X-RAY DIFFRACTIONf_angle_d1.1274771
X-RAY DIFFRACTIONf_dihedral_angle_d14.0781347
X-RAY DIFFRACTIONf_chiral_restr0.082483
X-RAY DIFFRACTIONf_plane_restr0.005644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.24541240.24162400X-RAY DIFFRACTION84
1.6276-1.65720.26241370.23162412X-RAY DIFFRACTION84
1.6572-1.68910.25621310.22312399X-RAY DIFFRACTION84
1.6891-1.72350.22271190.22452407X-RAY DIFFRACTION85
1.7235-1.7610.22431290.21272424X-RAY DIFFRACTION84
1.761-1.8020.23981260.22032442X-RAY DIFFRACTION86
1.802-1.8470.2291400.20442483X-RAY DIFFRACTION87
1.847-1.8970.21191230.18842515X-RAY DIFFRACTION88
1.897-1.95280.22881450.19072587X-RAY DIFFRACTION91
1.9528-2.01580.21581420.182676X-RAY DIFFRACTION94
2.0158-2.08780.2021380.17522787X-RAY DIFFRACTION96
2.0878-2.17140.19181320.17222801X-RAY DIFFRACTION97
2.1714-2.27010.19421480.17292824X-RAY DIFFRACTION98
2.2701-2.38980.22721450.17362858X-RAY DIFFRACTION98
2.3898-2.53940.19971470.18282842X-RAY DIFFRACTION98
2.5394-2.73530.22831520.18552844X-RAY DIFFRACTION99
2.7353-3.01030.19561650.18012878X-RAY DIFFRACTION99
3.0103-3.44520.19581450.16522911X-RAY DIFFRACTION99
3.4452-4.3380.15841430.14642955X-RAY DIFFRACTION99
4.338-27.92530.17641740.163073X-RAY DIFFRACTION99

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