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- PDB-4qrt: Crystal Structure of HLA B*0801 in complex with ELN_YYM, ELNRKMIYM -

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Basic information

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


: / regulation of viral process / 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 / detection of bacterium / secretory granule membrane ...: / regulation of viral process / 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 / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / 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 / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / host cell nucleus / Neutrophil degranulation / 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 / membrane / identical protein binding / nucleus / plasma membrane
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 / MHC class I-like antigen recognition-like ...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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Major immediate-early protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 1.0Jul 16, 2014Provider: repository / Type: Initial release

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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-8 alpha chain
B: Beta-2-microglobulin
C: Major immediate-early protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0694
Polymers45,0073
Non-polymers621
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-19 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.540, 81.580, 111.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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 Major immediate-early protein


Mass: 1199.486 Da / Num. of mol.: 1 / Fragment: unp residues 51-59 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 / References: UniProt: Q9YRL8
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.92 %
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: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.3→111.5 Å / Num. all: 111044 / Num. obs: 111044 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rsym value: 0.082

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XSCALEdata scaling
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.822 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 4515 5.01 %
Rwork0.1794 --
obs0.1806 90038 98.32 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.894 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 18.9744 Å2 / Biso min: 5.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.3976 Å2-0 Å20 Å2
2---1.4952 Å2-0 Å2
3---2.8928 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 4 638 3813

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