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- PDB-4huw: Crystal Structure of H2Db-NPM6T -

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Basic information

Entry
Database: PDB / ID: 4huw
TitleCrystal Structure of H2Db-NPM6T
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NPM6T 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 I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / viral penetration into host nucleus / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / host cell / sensory perception of smell / positive regulation of T cell activation / 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 / ribonucleoprotein complex / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / host cell nucleus / protein-containing complex binding / 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 / MHC class I-like antigen recognition-like ...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 / molecular replacement / Resolution: 3.16 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 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: NPM6T variant peptide
J: NPM6T variant peptide
K: NPM6T variant peptide
L: NPM6T variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,03617
Polymers181,55512
Non-polymers4805
Water3,801211
1
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
I: NPM6T variant peptide
J: NPM6T variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0669
Polymers90,7786
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-93 kcal/mol
Surface area35700 Å2
MethodPISA
2
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
K: NPM6T variant peptide
L: NPM6T variant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9708
Polymers90,7786
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-80 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 84.680, 136.420
Angle α, β, γ (deg.)90.00, 90.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32601.303 Da / Num. of mol.: 4
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.: 4
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
NPM6T variant peptide


Mass: 996.008 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: UniProt: Q5Q157*PLUS
#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.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.62 %
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: MX2 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 31034 / % possible obs: 94.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 54.19 Å2 / Rsym value: 0.117 / Net I/σ(I): 15.5

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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
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3cpl

3cpl


Resolution: 3.16→58.12 Å / Cor.coef. Fo:Fc: 0.9163 / Cor.coef. Fo:Fc free: 0.8577 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 1565 5.04 %RANDOM
Rwork0.1779 ---
obs0.1814 31034 98.58 %-
Displacement parametersBiso mean: 45.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.2795 Å20 Å20.0971 Å2
2--1.8844 Å20 Å2
3----7.164 Å2
Refine analyzeLuzzati coordinate error obs: 0.495 Å
Refinement stepCycle: LAST / Resolution: 3.16→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12660 0 25 211 12896
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113172HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1717905HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4515SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes360HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1884HARMONIC5
X-RAY DIFFRACTIONt_it13172HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion22.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1608SEMIHARMONIC5
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_contact15525SEMIHARMONIC4
LS refinement shellResolution: 3.16→3.26 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3495 128 5.22 %
Rwork0.2353 2325 -
all0.2411 2453 -
obs--98.58 %

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