[English] 日本語
Yorodumi
- PDB-1wbx: CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wbx
TitleCRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE
Components
  • BETA-2MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
  • INFLUENZA A PEPTIDE
KeywordsIMMUNE SYSTEM / MHC CLASS I / INFLUENZA PEPTIDE / HA468
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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to molecule of bacterial origin / regulation of erythrocyte differentiation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to molecule of bacterial origin / regulation of erythrocyte differentiation / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / T cell differentiation in thymus / positive regulation of T cell mediated cytotoxicity / viral budding from plasma membrane / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / protein refolding / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / host cell surface receptor binding / immune response / external side of plasma membrane / fusion of virus membrane with host plasma membrane / innate immune response / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / : / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 ...Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 / Hemagglutinin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMeijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Murine Mhc Class I H-2 D(B) and K(B) Molecules in Complex with Ctl Epitopes from Influenza a Virus: Implications for Tcr Repertoire Selection and Immunodominance
Authors: Meijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L.
History
DepositionNov 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
B: BETA-2MICROGLOBULIN
C: INFLUENZA A PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,9383
Polymers44,9383
Non-polymers00
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.759, 56.759, 275.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2245-

HOH

-
Components

#1: Protein H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN


Mass: 32087.703 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01899
#2: Protein BETA-2MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide INFLUENZA A PEPTIDE


Mass: 1146.294 Da / Num. of mol.: 1 / Fragment: RESIDUES 468-477 / Source method: obtained synthetically / Details: PEPTIDE DERIVED FROM PR8 INFLUENZA A HA468-477 / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: P26140
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
110 mMTris1droppH8.0
220 mg/mlprotein1drop
310-20 %(w/v)PEG80001reservoir
40.2 Mcalcium acetate1reservoiror magnesium acetate
50.1 Mcacodylate1reservoirpH6.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 32908 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 90.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 90.8 % / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPF

1jpf


Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.956 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3653 10 %RANDOM
Rwork0.198 ---
obs0.204 32908 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 515 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213257
X-RAY DIFFRACTIONr_bond_other_d0.0020.022800
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9244422
X-RAY DIFFRACTIONr_angle_other_deg0.82636541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84423.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54415544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.261524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_nbd_refined0.2120.2668
X-RAY DIFFRACTIONr_nbd_other0.2060.22919
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21513
X-RAY DIFFRACTIONr_nbtor_other0.0860.21919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2131.52469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36323102
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02431611
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.034.51320
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 251
Rwork0.238 2087
Software
*PLUS
Version: 5.2.0003 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.238

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more