[English] 日本語
Yorodumi
- PDB-1mwa: 2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mwa
Title2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX
Components
  • (2C T CELL RECEPTOR ...) x 2
  • DEV8
  • H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
  • MICROGLOBULIN MHC LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Ig domain / antigen recognition / complementarity determining region
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / respiratory chain complex IV / alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / respiratory chain complex IV / alpha-beta T cell receptor complex / 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 / T cell receptor complex / 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 / respiratory chain complex I / cellular defense response / Neutrophil degranulation / 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 / 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 / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / mitochondrial inner membrane / defense response to bacterium / external side of plasma membrane / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ 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 ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ 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
ACETIC ACID / : / : / T-cell receptor alpha chain V region PHDS58 / T-cell receptor beta-2 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Cytochrome c oxidase subunit NDUFA4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
CitationJournal: J.EXP.MED. / Year: 2002
Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation ...Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
Authors: Luz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
History
DepositionSep 27, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2002ID: 1JTR
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2C T CELL RECEPTOR ALPHA CHAIN
C: 2C T CELL RECEPTOR ALPHA CHAIN
B: 2C T CELL RECEPTOR BETA CHAIN
D: 2C T CELL RECEPTOR BETA CHAIN
H: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
I: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
L: MICROGLOBULIN MHC LIGHT CHAIN
M: MICROGLOBULIN MHC LIGHT CHAIN
P: DEV8
Q: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,30820
Polymers186,14210
Non-polymers3,16610
Water12,160675
1
A: 2C T CELL RECEPTOR ALPHA CHAIN
B: 2C T CELL RECEPTOR BETA CHAIN
H: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
L: MICROGLOBULIN MHC LIGHT CHAIN
P: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,55813
Polymers93,0715
Non-polymers2,4878
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2C T CELL RECEPTOR ALPHA CHAIN
D: 2C T CELL RECEPTOR BETA CHAIN
I: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
M: MICROGLOBULIN MHC LIGHT CHAIN
Q: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7507
Polymers93,0715
Non-polymers6792
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.899, 95.942, 84.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
2C T CELL RECEPTOR ... , 2 types, 4 molecules ACBD

#1: Protein 2C T CELL RECEPTOR ALPHA CHAIN / 2C alpha chain


Mass: 22298.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 224220, UniProt: P01738*PLUS
#2: Protein 2C T CELL RECEPTOR BETA CHAIN / 2C beta chain


Mass: 26284.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 1791255, UniProt: P01851*PLUS

-
Protein , 2 types, 4 molecules HILM

#3: Protein H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN / H-2Kbm3 heavy chain / H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN / K-B ALPHA CHAIN


Mass: 31719.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01901
#4: Protein MICROGLOBULIN MHC LIGHT CHAIN / microglobulin light chain


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01887

-
Protein/peptide , 1 types, 2 molecules PQ

#5: Protein/peptide DEV8


Mass: 1064.168 Da / Num. of mol.: 2 / Fragment: residues 54-61 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The peptide is naturally found in Mus musculus (Mouse).
References: UniProt: Q62425

-
Sugars , 3 types, 6 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: 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.: 1
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

-
Non-polymers , 3 types, 679 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 277.16 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M TRIS ACETATE, 12% PEG4000, 18% glycerol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.16K

-
Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationMonochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 95548 / % possible obs: 99.5 % / Rsym value: 0.052 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.453 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43932 / ESU R Free: 0.2997 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31273 4781 5 %RANDOM
Rwork0.28398 ---
obs0.28543 90694 100 %-
Displacement parametersBiso mean: 47.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--2.81 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13089 0 209 675 13973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.633
X-RAY DIFFRACTIONr_chiral_restr0.094

+
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