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- PDB-3bw9: Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer pep... -

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Basic information

Entry
Database: PDB / ID: 3bw9
TitleCrystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the pp65 protein
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • CPS peptide from 65 kDa lower matrix phosphoprotein
  • HLA class I histocompatibility antigen, B-35 alpha chain
KeywordsIMMUNE SYSTEM / HLA B*3508 / HCMV / pp65 / immunology / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Ubl conjugation / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Phosphoprotein / Tegument protein / Viral matrix protein / Virion
Function / homology
Function and homology information


viral tegument / 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 ...viral tegument / 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 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / structural constituent of virion / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / 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
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 / 65 kDa phosphoprotein / 65 kDa phosphoprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWynn, K.K. / Marland, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. ...Wynn, K.K. / Marland, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Khanna, R.
CitationJournal: Blood / Year: 2008
Title: Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection
Authors: Wynn, K.K. / Fulton, Z. / Cooper, L. / Silins, S.L. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Miles, J.J. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Khanna, R.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: CPS peptide from 65 kDa lower matrix phosphoprotein


Theoretical massNumber of molelcules
Total (without water)45,2803
Polymers45,2803
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-20.1 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.006, 82.086, 111.515
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-35 alpha chain / HLA B*3508 heavy chain / MHC class I antigen B*35


Mass: 31984.281 Da / Num. of mol.: 1 / Fragment: residues in database 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / 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) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide CPS peptide from 65 kDa lower matrix phosphoprotein / CPS peptide from HCMV pp65 protein


Mass: 1416.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P06725, UniProt: P18139*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS VARIANT, B*3508.

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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: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M ammonium acetate, 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Nov 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 94441 / % possible obs: 98.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.4
Reflection shellResolution: 1.72→1.82 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.334 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H6P

2h6p


Resolution: 1.75→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.618 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2395 5.1 %RANDOM
Rwork0.189 ---
obs0.192 47354 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.782 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 0 438 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213794
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9385218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06323210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49315638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111544
X-RAY DIFFRACTIONr_chiral_restr0.0940.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023154
X-RAY DIFFRACTIONr_nbd_refined0.2320.31825
X-RAY DIFFRACTIONr_nbtor_refined0.3170.52580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5685
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.545
X-RAY DIFFRACTIONr_mcbond_it1.07722321
X-RAY DIFFRACTIONr_mcangle_it1.66833717
X-RAY DIFFRACTIONr_scbond_it1.74431695
X-RAY DIFFRACTIONr_scangle_it2.33541501
LS refinement shellResolution: 1.75→1.811 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.307 226 -
Rwork0.246 4207 -
all-4433 -
obs--97.17 %

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