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- PDB-5wmn: Crystal Structure of HLA-B7 in complex with SPI, an influenza peptide -

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Basic information

Entry
Database: PDB / ID: 5wmn
TitleCrystal Structure of HLA-B7 in complex with SPI, an influenza peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • SPI peptide from Influenza A virus
KeywordsIMMUNE SYSTEM / HLA / viral peptide / IAV / EBV / CMV / crossreactivity / TCR / T cell / heterologous immunity
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 / 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 ...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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsGras, S. / Rossjohn, J.
CitationJournal: J. Immunol. / Year: 2018
Title: Inability To Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity among Common Viruses.
Authors: Rowntree, L.C. / Nguyen, T.H.O. / Halim, H. / Purcell, A.W. / Rossjohn, J. / Gras, S. / Kotsimbos, T.C. / Mifsud, N.A.
History
DepositionJul 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-7 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B-7 alpha chain
D: Beta-2-microglobulin
E: SPI peptide from Influenza A virus
F: SPI peptide from Influenza A virus


Theoretical massNumber of molelcules
Total (without water)89,8616
Polymers89,8616
Non-polymers00
Water12,412689
1
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
E: SPI peptide from Influenza A virus


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-22 kcal/mol
Surface area19230 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B-7 alpha chain
D: Beta-2-microglobulin
F: SPI peptide from Influenza A virus


Theoretical massNumber of molelcules
Total (without water)44,9313
Polymers44,9313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-25 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.396, 84.262, 77.945
Angle α, β, γ (deg.)90.000, 104.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 32059.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide SPI peptide from Influenza A virus


Mass: 992.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.46 Å3/Da / Density % sol: 50.01 % / Mosaicity: 0.24 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-24%PEG4000, 0.2 NH4 Acetate, 0.1M Na-cacodylate pH 6.5

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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: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.82→47.61 Å / Num. obs: 77499 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.8 / Num. measured all: 292026 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.82-1.863.70.7311608044020.7692.196.1
9.1-47.613.10.01819316150.99967.593.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vcl

3vcl


Resolution: 1.82→36.81 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9262 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 3878 5.01 %RANDOM
Rwork0.1841 ---
obs0.1859 77437 99.27 %-
Displacement parametersBiso max: 110.85 Å2 / Biso mean: 32.82 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-6.1376 Å20 Å21.6825 Å2
2---7.4976 Å20 Å2
3---1.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: final / Resolution: 1.82→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 0 689 6995
Biso mean---39.41 -
Num. residues----769
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2332SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes198HARMONIC2
X-RAY DIFFRACTIONt_gen_planes989HARMONIC5
X-RAY DIFFRACTIONt_it6640HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7885SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6640HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9058HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion16.38
LS refinement shellResolution: 1.82→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2452 301 5.39 %
Rwork0.2209 5284 -
all0.2222 5585 -
obs--99.27 %

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