[English] 日本語
Yorodumi
- PDB-1bqh: MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bqh
TitleMURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8
Components
  • PROTEIN (BETA-2-MICROGLOBULIN )
  • PROTEIN (CD8A OR LYT2 OR LYT-2)
  • PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
  • PROTEIN (VSV8)
KeywordsIMMUNE SYSTEM / T-CELL / CORECEPTOR / GLYCOPROTEIN / COMPLEX / IMMUNOLOGY / ANTIGEN
Function / homology
Function and homology information


cytotoxic T cell differentiation / T cell mediated immunity / 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 exogenous peptide antigen via MHC class I / inner ear development ...cytotoxic T cell differentiation / T cell mediated immunity / 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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / positive regulation of calcium-mediated signaling / T cell activation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / calcium-mediated signaling / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading 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 / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / protein refolding / protein homotetramerization / defense response to virus / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to bacterium / external side of plasma membrane / structural molecule activity / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
CD8 alpha subunit / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : ...CD8 alpha subunit / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
T-cell surface glycoprotein CD8 alpha chain / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, J.H. / Reinherz, E.L. / Kern, P.S. / Chang, H.C.
CitationJournal: Immunity / Year: 1998
Title: Structural basis of CD8 coreceptor function revealed by crystallographic analysis of a murine CD8alphaalpha ectodomain fragment in complex with H-2Kb.
Authors: Kern, P.S. / Teng, M.K. / Smolyar, A. / Liu, J.H. / Liu, J. / Hussey, R.E. / Spoerl, R. / Chang, H.C. / Reinherz, E.L. / Wang, J.H.
History
DepositionAug 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (BETA-2-MICROGLOBULIN )
C: PROTEIN (VSV8)
D: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
E: PROTEIN (BETA-2-MICROGLOBULIN )
F: PROTEIN (VSV8)
G: PROTEIN (CD8A OR LYT2 OR LYT-2)
H: PROTEIN (CD8A OR LYT2 OR LYT-2)
I: PROTEIN (CD8A OR LYT2 OR LYT-2)
K: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,55314
Polymers146,66810
Non-polymers8854
Water00
1
A: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (BETA-2-MICROGLOBULIN )
C: PROTEIN (VSV8)
G: PROTEIN (CD8A OR LYT2 OR LYT-2)
H: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7767
Polymers73,3345
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)
E: PROTEIN (BETA-2-MICROGLOBULIN )
F: PROTEIN (VSV8)
I: PROTEIN (CD8A OR LYT2 OR LYT-2)
K: PROTEIN (CD8A OR LYT2 OR LYT-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7767
Polymers73,3345
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.900, 98.400, 170.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN)


Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01901
#2: Protein PROTEIN (BETA-2-MICROGLOBULIN )


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01887
#3: Protein/peptide PROTEIN (VSV8)


Mass: 956.078 Da / Num. of mol.: 2 / Fragment: ANTIGENIC PEPTIDE / Source method: obtained synthetically
#4: Protein
PROTEIN (CD8A OR LYT2 OR LYT-2)


Mass: 14512.637 Da / Num. of mol.: 4 / Fragment: IG ECTODOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: GENE FUSED TO THROMBIN CLEAVAGE SITE AND LEUCINE ZIPPER
Cell line (production host): CHO LEC 3.2.8.1 / Gene (production host): CD8A / Production host: Mus musculus (house mouse) / References: UniProt: P01731
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.5 / Details: 20-25% PEG 4K, 0.2M LI2SO4, 0.1M TRIS PH8.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMHEPES1drop
320-25 %PEG40001reservoir
40.2 M1reservoirLi2SO4
50.1 MTris1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 34131 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.249 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 99259 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 90.7 % / Rmerge(I) obs: 0.249

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAA

2vaa


Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3285 10.1 %RANDOM
Rwork0.212 ---
obs0.212 32467 88.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10148 0 56 0 10204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.511
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH3.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.511

+
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