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- PDB-3e3q: Structure of the 3alpham13 high-affinity mutant of the 2C TCR in ... -

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Basic information

Entry
Database: PDB / ID: 3e3q
TitleStructure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9
Components
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • QL9 peptide
  • T-cell receptor alpha chain V region PHDS58
  • TCR beta chain
KeywordsIMMUNE SYSTEM / TCR / MHC / high affinity / cross reactivity / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Receptor
Function / homology
Function and homology information


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 ...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 / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / T cell receptor complex / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / protein-folding chaperone binding / antibacterial humoral response / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
Similarity search - Function
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 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...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 / 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 / H-2 class I histocompatibility antigen, L-D alpha chain / TRAV9-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsColf, L.A. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2008
Title: Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation.
Authors: Jones, L.L. / Colf, L.A. / Stone, J.D. / Garcia, K.C. / Kranz, D.M.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, L-D alpha chain
Q: QL9 peptide
D: T-cell receptor alpha chain V region PHDS58
E: TCR beta chain
B: H-2 class I histocompatibility antigen, L-D alpha chain
G: QL9 peptide
C: T-cell receptor alpha chain V region PHDS58
F: TCR beta chain
c: H-2 class I histocompatibility antigen, L-D alpha chain
f: QL9 peptide
d: T-cell receptor alpha chain V region PHDS58
e: TCR beta chain
H: H-2 class I histocompatibility antigen, L-D alpha chain
K: QL9 peptide
I: T-cell receptor alpha chain V region PHDS58
J: TCR beta chain
L: H-2 class I histocompatibility antigen, L-D alpha chain
O: QL9 peptide
M: T-cell receptor alpha chain V region PHDS58
N: TCR beta chain
P: H-2 class I histocompatibility antigen, L-D alpha chain
T: QL9 peptide
R: T-cell receptor alpha chain V region PHDS58
S: TCR beta chain
U: H-2 class I histocompatibility antigen, L-D alpha chain
X: QL9 peptide
V: T-cell receptor alpha chain V region PHDS58
W: TCR beta chain
Y: H-2 class I histocompatibility antigen, L-D alpha chain
b: QL9 peptide
Z: T-cell receptor alpha chain V region PHDS58
a: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)365,72432
Polymers365,72432
Non-polymers00
Water0
1
A: H-2 class I histocompatibility antigen, L-D alpha chain
Q: QL9 peptide
D: T-cell receptor alpha chain V region PHDS58
E: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H-2 class I histocompatibility antigen, L-D alpha chain
G: QL9 peptide
C: T-cell receptor alpha chain V region PHDS58
F: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
c: H-2 class I histocompatibility antigen, L-D alpha chain
f: QL9 peptide
d: T-cell receptor alpha chain V region PHDS58
e: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: H-2 class I histocompatibility antigen, L-D alpha chain
K: QL9 peptide
I: T-cell receptor alpha chain V region PHDS58
J: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
L: H-2 class I histocompatibility antigen, L-D alpha chain
O: QL9 peptide
M: T-cell receptor alpha chain V region PHDS58
N: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: H-2 class I histocompatibility antigen, L-D alpha chain
T: QL9 peptide
R: T-cell receptor alpha chain V region PHDS58
S: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
U: H-2 class I histocompatibility antigen, L-D alpha chain
X: QL9 peptide
V: T-cell receptor alpha chain V region PHDS58
W: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
Y: H-2 class I histocompatibility antigen, L-D alpha chain
b: QL9 peptide
Z: T-cell receptor alpha chain V region PHDS58
a: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7164
Polymers45,7164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.472, 160.458, 357.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein
H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 20541.621 Da / Num. of mol.: 8 / Fragment: UNP residues 25-199
Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, I66V, W97R, K131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01897
#2: Protein/peptide
QL9 peptide


Mass: 1063.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse
#3: Protein
T-cell receptor alpha chain V region PHDS58


Mass: 12071.595 Da / Num. of mol.: 8 / Mutation: L43P, W82R, G99D F100P A101P S102P A103L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01738, UniProt: Q5R1C2*PLUS
#4: Protein
TCR beta chain


Mass: 12039.129 Da / Num. of mol.: 8 / Mutation: G17E, G42E, H47Y, I77T, L81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium citrate, 20% PEG 3350, 3% trimethyl amine N-oxide dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 93313 / % possible obs: 97.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Χ2: 1.117 / Net I/σ(I): 10.3
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2 / Num. unique all: 9386 / Χ2: 1.005 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OI9

2oi9


Resolution: 2.95→41.52 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4687 4.9 %5%
Rwork0.25 ---
obs-93313 97.4 %-
Solvent computationBsol: 23.072 Å2
Displacement parametersBiso max: 100.58 Å2 / Biso mean: 47.947 Å2 / Biso min: 18.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.959 Å20 Å20 Å2
2--1.017 Å20 Å2
3----6.976 Å2
Refinement stepCycle: LAST / Resolution: 2.95→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25808 0 0 0 25808
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.465
X-RAY DIFFRACTIONc_mcbond_it1.2481.5
X-RAY DIFFRACTIONc_scbond_it1.7472
X-RAY DIFFRACTIONc_mcangle_it2.2032
X-RAY DIFFRACTIONc_scangle_it2.8042.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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