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- PDB-4hv8: Crystal Structure of H2Db-H155A-NPM6I -

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Basic information

Entry
Database: PDB / ID: 4hv8
TitleCrystal Structure of H2Db-H155A-NPM6I
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NPM6I variant peptide
KeywordsIMMUNE SYSTEM / viral immunity / T cell / H2Db / influenza / viral escape
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / 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 / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / host cell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / ribonucleoprotein complex / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2 Å
AuthorsGras, S. / Twist, K.A. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Preemptive priming readily overcomes structure-based mechanisms of virus escape.
Authors: Valkenburg, S.A. / Gras, S. / Guillonneau, C. / Hatton, L.A. / Bird, N.A. / Twist, K.A. / Halim, H. / Jackson, D.C. / Purcell, A.W. / Turner, S.J. / Doherty, P.C. / Rossjohn, J. / Kedzierska, K.
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Oct 30, 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: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: NPM6I variant peptide
F: NPM6I variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,24412
Polymers90,6686
Non-polymers5766
Water14,952830
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: NPM6I variant peptide
hetero molecules

A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: NPM6I variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,43614
Polymers90,6686
Non-polymers7698
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12410 Å2
ΔGint-150 kcal/mol
Surface area36510 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: NPM6I variant peptide
hetero molecules

C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: NPM6I variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,05210
Polymers90,6686
Non-polymers3844
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10590 Å2
ΔGint-83 kcal/mol
Surface area37590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.920, 72.930, 86.380
Angle α, β, γ (deg.)90.00, 103.11, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32534.236 Da / Num. of mol.: 2 / Mutation: H155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide NPM6I variant peptide


Mass: 1008.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: Q5Q157*PLUS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 0.2M LiSO4, 25-30% PEG 8000, pH 8.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 68339 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 31.85 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.10.4832.84199.9
2.1-2.20.3683.661100
2.2-2.30.3284.83199.1
2.3-2.50.1827.12199.9
2.5-2.60.139.75199.8
2.6-2.70.10511.541100
2.7-30.07815.22199.4
3-40.04524.26198.3
4-50.0333.37197.6
5-60.02733.79198.6
6-100.02434.67199.6
100.01937.51195.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
BUSTER2.10.0refinement
RefinementStarting model: PDB entry 3cpl

3cpl


Resolution: 2→72.93 Å / Cor.coef. Fo:Fc: 0.9475 / Cor.coef. Fo:Fc free: 0.9182 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 3463 5.07 %RANDOM
Rwork0.1807 ---
obs0.1835 68324 99.31 %-
Displacement parametersBiso mean: 36.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.0492 Å20 Å2-1.4459 Å2
2---6.7957 Å20 Å2
3---4.7465 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2→72.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6317 0 30 830 7177
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016612HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.098988HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2289SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes951HARMONIC5
X-RAY DIFFRACTIONt_it6612HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion17.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion811SEMIHARMONIC5
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_contact8205SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2646 246 4.88 %
Rwork0.2248 4790 -
all0.2267 5036 -
obs--99.31 %

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