[English] 日本語
Yorodumi
- PDB-2ckb: STRUCTURE OF THE 2C/KB/DEV8 COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ckb
TitleSTRUCTURE OF THE 2C/KB/DEV8 COMPLEX
Components
  • (ALPHA, BETA T CELL ...) x 2
  • BETA-2 MICROGLOBULIN
  • DEV8 PEPTIDE
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
KeywordsMAJOR HISTOCOMPATIBILITY COMPLEX / T CELL ANTIGEN RECEPTOR
Function / homology
Function and homology information


positive regulation of cytochrome-c oxidase activity / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex IV / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production ...positive regulation of cytochrome-c oxidase activity / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex IV / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / mitochondrial respiratory chain complex I / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / mitochondrial membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway
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 / Immunoglobulin V-Type / Beta-2-Microglobulin ...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 subtype / Immunoglobulin / 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
: / : / T-cell receptor alpha chain V region PHDS58 / 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: 3 Å
AuthorsGarcia, K.C. / Degano, M. / Wilson, I.A.
Citation
Journal: Science / Year: 1998
Title: Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen.
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#1: Journal: Science / Year: 1996
Title: An Alphabeta T Cell Receptor Structure at 2.5 A and its Orientation in the Tcr-Mhc Complex
Authors: Garcia, K.C. / Degano, M. / Stanfield, R.L. / Brunmark, A. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
History
DepositionJan 14, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA, BETA T CELL RECEPTOR
B: ALPHA, BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
P: DEV8 PEPTIDE
L: BETA-2 MICROGLOBULIN
C: ALPHA, BETA T CELL RECEPTOR
D: ALPHA, BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
Q: DEV8 PEPTIDE
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)186,00010
Polymers186,00010
Non-polymers00
Water1086
1
A: ALPHA, BETA T CELL RECEPTOR
B: ALPHA, BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
P: DEV8 PEPTIDE
L: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)93,0005
Polymers93,0005
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ALPHA, BETA T CELL RECEPTOR
D: ALPHA, BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
Q: DEV8 PEPTIDE
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)93,0005
Polymers93,0005
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)295.660, 89.960, 84.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.961149, 0.275631, -0.014864), (-0.275712, 0.961233, -0.003698), (0.013268, 0.007653, 0.999883)-202.06081, 47.5935, -48.5005
2given(0.963537, 0.266972, -0.017951), (-0.267279, 0.963457, -0.017688), (0.012572, 0.021841, 0.999682)-201.83701, 46.7915, -49.1706
3given(0.959949, 0.279146, -0.023998), (-0.279589, 0.959959, -0.017589), (0.018127, 0.023594, 0.999557)-201.18221, 50.1028, -50.9724
4given(0.966869, 0.253587, -0.029307), (-0.254435, 0.96662, -0.030144), (0.020684, 0.036602, 0.999116)-200.733, 44.0797, -52.3646
5given(0.947092, 0.320962, -0.000891), (-0.320963, 0.947085, -0.003616), (-0.000316, 0.003711, 0.999993)-202.0744, 61.4576, -44.2977
6given(0.948063, 0.318082, -0.000309), (-0.31807, 0.948034, 0.007925), (0.002813, -0.007415, 0.999969)-202.2825, 60.2545, -44.4623

-
Components

-
ALPHA, BETA T CELL ... , 2 types, 4 molecules ACBD

#1: Protein ALPHA, BETA T CELL RECEPTOR / T CELL ANTIGEN RECEPTOR


Mass: 22298.889 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Details: VB8.2DB2JB2.4CB2\;VA3JA58CA / Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Cellular location: EXTRACELLULARGlossary of biology / Production host: Drosophila melanogaster (fruit fly) / References: EMBL: X01134, UniProt: P01738*PLUS
#2: Protein ALPHA, BETA T CELL RECEPTOR / T CELL ANTIGEN RECEPTOR


Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Details: VB8.2DB2JB2.4CB2\;VA3JA58CA / Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Cellular location: EXTRACELLULARGlossary of biology / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 1791255

-
Protein , 2 types, 4 molecules HILM

#3: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B) / MHC CLASS I


Mass: 31648.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ANTIGEN PRESENTING MOLECULE / Source: (gene. exp.) Mus musculus (house mouse) / Cell: NUCLEATED CELLS / Cellular location: EXTRACELLULARGlossary of biology / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901
#5: Protein BETA-2 MICROGLOBULIN / / BETA2M / B2M


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: NUCLEATED CELLS / Cellular location: EXTRACELLULARGlossary of biology / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887

-
Protein/peptide / Non-polymers , 2 types, 8 molecules PQ

#4: Protein/peptide DEV8 PEPTIDE / DEV8


Mass: 1064.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEPTIDE DERIVED FROM A MITOCHONDRIAL PROTEIN / References: UniProt: Q62425*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M TRIS ACETATE PH 7.2 0.1 M SODIUM CHLORIDE 12 % PEG 4000 AND TRANSFERRED IN ETHYLENE GLYCOL CONTAINING PRECIPITANT SOLUTION, FROM 4% TO 22%, BEFORE DATA COLLECTION.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mphosphate1reservoir
21.0 %methylpentanediol1reservoir

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 314268 / % possible obs: 83.3 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.088 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.12 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.328 / % possible all: 70.1
Reflection
*PLUS
Num. obs: 37960 / Num. measured all: 314268 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 70.1 % / Rmerge(I) obs: 0.33

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TCR, 1VAC

1tcr

1vac


Resolution: 3→25 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1435 4 %SPHERES
Rwork0.221 ---
obs0.221 34092 78.7 %-
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-14.6 Å20 Å20 Å2
2---11 Å20 Å2
3---14.9 Å2
Refine analyzeLuzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13104 0 0 6 13110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it9.941.5
X-RAY DIFFRACTIONx_mcangle_it14.72
X-RAY DIFFRACTIONx_scbond_it15.62
X-RAY DIFFRACTIONx_scangle_it20.62.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINED8.530.042300
2214.20.064150
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 143 -
Rwork0.322 3499 -
obs--67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

+
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