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- PDB-4l8d: Crystal structure of the H2Db in complex with the NP-N5D peptide -

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Basic information

Entry
Database: PDB / ID: 4l8d
TitleCrystal structure of the H2Db in complex with the NP-N5D peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NP-N5D peptide
KeywordsIMMUNE SYSTEM / Influenza / viral escape / T cell immunity
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRossjohn, J. / Gras, S.
CitationJournal: Nat Commun / Year: 2013
Title: Acute emergence and reversion of influenza A virus quasispecies within CD8(+) T cell antigenic peptides.
Authors: Valkenburg, S.A. / Quinones-Parra, S. / Gras, S. / Komadina, N. / McVernon, J. / Wang, Z. / Halim, H. / Iannello, P. / Cole, C. / Laurie, K. / Kelso, A. / Rossjohn, J. / Doherty, P.C. / ...Authors: Valkenburg, S.A. / Quinones-Parra, S. / Gras, S. / Komadina, N. / McVernon, J. / Wang, Z. / Halim, H. / Iannello, P. / Cole, C. / Laurie, K. / Kelso, A. / Rossjohn, J. / Doherty, P.C. / Turner, S.J. / Kedzierska, K.
History
DepositionJun 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: NP-N5D peptide
F: NP-N5D peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,88311
Polymers90,4036
Non-polymers4805
Water16,646924
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: NP-N5D peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3945
Polymers45,2023
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-38 kcal/mol
Surface area19370 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: NP-N5D peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4906
Polymers45,2023
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-50 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.343, 136.132, 80.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-180-

HOH

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / heavy chain H2Db / H-2D(B)


Mass: 32470.111 Da / Num. of mol.: 2 / Fragment: UNP residues 25-304
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 / b2m


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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 NP-N5D peptide


Mass: 1027.084 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN CHAINS B AND D, A85D (UNP A105D) IS A NATURAL VARIANT.

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M lithium sulfate, 25-30% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.9→136.132 Å / Num. all: 74976 / Num. obs: 74976 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.126
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.12data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HUU

4huu


Resolution: 1.9→80.87 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9254 / Occupancy max: 1 / Occupancy min: 0.03 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.157 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3775 5.04 %RANDOM
Rwork0.1879 ---
obs0.1899 74913 99.98 %-
Displacement parametersBiso mean: 31.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.3993 Å20 Å20 Å2
2---0.5495 Å20 Å2
3---0.1502 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: LAST / Resolution: 1.9→80.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 25 924 7255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016667HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.049077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2304SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes963HARMONIC5
X-RAY DIFFRACTIONt_it6667HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion810SEMIHARMONIC5
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_contact8344SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2627 280 5.11 %
Rwork0.2306 5198 -
all0.2323 5478 -
obs--99.98 %

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