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- PDB-4qrs: Crystal Structure of HLA B*0801 in complex with ELK_IYM, ELKRKMIYM -

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Basic information

Entry
Database: PDB / ID: 4qrs
TitleCrystal Structure of HLA B*0801 in complex with ELK_IYM, ELKRKMIYM
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


symbiont-mediated perturbation of host cell cycle progression / DNA-templated viral transcription / 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 ...symbiont-mediated perturbation of host cell cycle progression / DNA-templated viral transcription / 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 / 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 / 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 / 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 / membrane / plasma membrane / cytosol
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 / 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 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Oct 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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)45,0845
Polymers44,9663
Non-polymers1182
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-25 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 81.290, 111.220
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: 11823.251 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: 1214.563 Da / Num. of mol.: 1 / Fragment: unp residues 51-59 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 / References: UniProt: Q9YRL3
#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.: 553 / 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: 51.76 %
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 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 622396 / Num. obs: 90760 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.36
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.50.4963.35198.2
1.5-1.70.2578.041100
1.7-1.90.12414.961100
1.9-20.08121.341100
2-2.10.07124.351100
2.1-2.20.06326.791100
2.2-2.50.05529.651100
2.5-30.04933.451100
3-40.04237.31199.9
4-60.03839.05199
6-100.03737.64196.5
100.0433.16169.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.761 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 4547 5.01 %
Rwork0.1932 --
obs0.1944 90755 99.52 %
all-90760 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.062 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4557 Å20 Å2-0 Å2
2---2.2393 Å20 Å2
3---4.695 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 8 553 3729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063564
X-RAY DIFFRACTIONf_angle_d1.0194879
X-RAY DIFFRACTIONf_dihedral_angle_d12.5161392
X-RAY DIFFRACTIONf_chiral_restr0.075493
X-RAY DIFFRACTIONf_plane_restr0.004662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.37671390.35642551X-RAY DIFFRACTION90
1.4159-1.43260.3341340.32662838X-RAY DIFFRACTION99
1.4326-1.450.35751220.30962943X-RAY DIFFRACTION100
1.45-1.46840.29751340.29792813X-RAY DIFFRACTION100
1.4684-1.48770.26311570.26732869X-RAY DIFFRACTION100
1.4877-1.50810.28551470.26682844X-RAY DIFFRACTION100
1.5081-1.52960.28291450.24732891X-RAY DIFFRACTION100
1.5296-1.55240.25311620.23562813X-RAY DIFFRACTION100
1.5524-1.57670.23121440.22752860X-RAY DIFFRACTION100
1.5767-1.60250.23681530.23192855X-RAY DIFFRACTION100
1.6025-1.63010.24991540.21932897X-RAY DIFFRACTION100
1.6301-1.65980.24991590.21122823X-RAY DIFFRACTION100
1.6598-1.69170.23361460.20342903X-RAY DIFFRACTION100
1.6917-1.72620.23321540.19982843X-RAY DIFFRACTION100
1.7262-1.76370.19971500.19742872X-RAY DIFFRACTION100
1.7637-1.80470.21351680.20412843X-RAY DIFFRACTION100
1.8047-1.84980.27311430.20292886X-RAY DIFFRACTION100
1.8498-1.89980.21661470.20052863X-RAY DIFFRACTION100
1.8998-1.95560.25781560.20792905X-RAY DIFFRACTION100
1.9556-2.01870.22041670.20682839X-RAY DIFFRACTION100
2.0187-2.09070.24651380.20452918X-RAY DIFFRACTION100
2.0907-2.17440.23221460.19692865X-RAY DIFFRACTION100
2.1744-2.27320.22621540.18812910X-RAY DIFFRACTION100
2.2732-2.39280.2031730.18312900X-RAY DIFFRACTION100
2.3928-2.54250.21381640.18352901X-RAY DIFFRACTION100
2.5425-2.73830.21141540.18492909X-RAY DIFFRACTION100
2.7383-3.0130.20071690.18582912X-RAY DIFFRACTION100
3.013-3.4470.20451440.17472951X-RAY DIFFRACTION100
3.447-4.33530.15671510.15132989X-RAY DIFFRACTION100
4.3353-19.76260.18881730.17253002X-RAY DIFFRACTION97

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