[English] 日本語
Yorodumi
- PDB-6h6h: Crystal structures of the murine class I major histocompatibility... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h6h
TitleCrystal structures of the murine class I major histocompatibility complex H-2Dbm13 in complex with adenovirus-derived peptide Ad10
Components
  • Beta-2-microglobulin
  • H-2D cell surface glycoprotein
  • SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
KeywordsIMMUNE SYSTEM / MHC class I / adenovirus
Function / homology
Function and homology information


regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / molecular sequestering activity / antigen processing and presentation of peptide antigen via MHC class I / 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 ...regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / molecular sequestering activity / antigen processing and presentation of peptide antigen via MHC class I / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / cellular defense response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / 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 / 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 / symbiont-mediated suppression of host gene expression / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / regulation of protein localization / iron ion transport / T cell differentiation in thymus / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA-binding transcription factor binding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / external side of plasma membrane / lysosomal membrane / virus-mediated perturbation of host defense response / positive regulation of cell population proliferation / regulation of DNA-templated transcription / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / cytosol
Similarity search - Function
Adenovirus early E1A protein / Early E1A 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 / : ...Adenovirus early E1A protein / Early E1A 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / Early E1A protein / H-2D cell surface glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified adenovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAchour, A. / Sandalova, T. / Han, X.
CitationJournal: to be published
Title: Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity
Authors: Abualrous, E.T. / Han, X. / Badia-Martines, D. / Sun, R. / van Hall, T. / Sandalova, T. / Ossendorp, F. / Achour, A.
History
DepositionJul 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2D cell surface glycoprotein
D: H-2D cell surface glycoprotein
B: Beta-2-microglobulin
E: Beta-2-microglobulin
C: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
F: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,96223
Polymers102,3376
Non-polymers1,62517
Water3,513195
1
A: H-2D cell surface glycoprotein
B: Beta-2-microglobulin
C: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,31315
Polymers51,1683
Non-polymers1,14512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-132 kcal/mol
Surface area19520 Å2
MethodPISA
2
D: H-2D cell surface glycoprotein
E: Beta-2-microglobulin
F: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6498
Polymers51,1683
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-100 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.410, 70.270, 87.050
Angle α, β, γ (deg.)83.98, 86.90, 81.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODB1 - 2761 - 276
12ILEILEMETMETBC1 - 991 - 99
22ILEILEMETMETED1 - 991 - 99

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein H-2D cell surface glycoprotein


Mass: 38466.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H-2D, H2-L / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q31167
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01887

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE


Mass: 998.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus / References: UniProt: P03255*PLUS

-
Non-polymers , 3 types, 212 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.8M ammonium sulphate, 0.1M Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 42580 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rsym value: 0.121 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.57 Å / Rsym value: 0.57

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5A

1n5a


Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.329 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24869 2133 5.1 %RANDOM
Rwork0.20012 ---
obs0.2026 39771 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.06 Å2-0.04 Å2
2---0.22 Å20.28 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 87 195 6548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196540
X-RAY DIFFRACTIONr_bond_other_d0.0040.025839
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9498888
X-RAY DIFFRACTIONr_angle_other_deg1.11313481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74223.728338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.054151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2781548
X-RAY DIFFRACTIONr_chiral_restr0.0840.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217326
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021566
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1245.2063046
X-RAY DIFFRACTIONr_mcbond_other3.1245.2063045
X-RAY DIFFRACTIONr_mcangle_it5.0227.7923794
X-RAY DIFFRACTIONr_mcangle_other5.0217.7923795
X-RAY DIFFRACTIONr_scbond_it3.4985.6673494
X-RAY DIFFRACTIONr_scbond_other3.4975.6673494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.688.3355094
X-RAY DIFFRACTIONr_long_range_B_refined8.6840.5256992
X-RAY DIFFRACTIONr_long_range_B_other8.6840.5286991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A31012
12D31012
21B11650
22E11650
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.299 2895 -
obs--96.83 %

+
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