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- PDB-4n5e: 42F3 TCR pCPA12/H-2Ld complex -

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Basic information

Entry
Database: PDB / ID: 4n5e
Title42F3 TCR pCPA12/H-2Ld complex
Components
  • 42F3 alpha VmCh
  • 42F3 beta VmCh
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • pCPA12
KeywordsIMMUNE SYSTEM / Ig / TCR / MHC / antigen
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 lectin-like receptor binding / natural killer cell tolerance induction / T cell receptor complex ...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 lectin-like receptor binding / natural killer cell tolerance induction / T cell receptor complex / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / 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 interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / 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 / T cell receptor binding / 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 / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / cell surface receptor signaling pathway / 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
Domain of unknown function (DUF1968) / 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 ...Domain of unknown function (DUF1968) / 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 beta, variable 13-1 / T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.059 Å
AuthorsBirnbaum, M.E. / Adams, J.J. / Garcia, K.C.
CitationJournal: Nat. Immunol. / Year: 2016
Title: Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.
Authors: Adams, J.J. / Narayanan, S. / Birnbaum, M.E. / Sidhu, S.S. / Blevins, S.J. / Gee, M.H. / Sibener, L.V. / Baker, B.M. / Kranz, D.M. / Garcia, K.C.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 42F3 alpha VmCh
D: 42F3 beta VmCh
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: pCPA12


Theoretical massNumber of molelcules
Total (without water)72,7924
Polymers72,7924
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.570, 101.570, 327.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody 42F3 alpha VmCh


Mass: 23383.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: P01738*PLUS
#2: Protein 42F3 beta VmCh


Mass: 27248.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075B5I3*PLUS
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 21115.303 Da / Num. of mol.: 1 / Fragment: UNP residues 25-203 / Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, 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) / References: UniProt: P01897
#4: Protein/peptide pCPA12


Mass: 1044.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide

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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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% PEG 3350, 100mM TRIS, pH 7.5 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.06→109.11 Å / Num. all: 19837 / Num. obs: 19619 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.06→3.22 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.059→59.895 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1003 5.13 %random
Rwork0.1938 ---
obs0.1956 19555 98.72 %-
all-19808 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.059→59.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4947 0 0 0 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055084
X-RAY DIFFRACTIONf_angle_d0.8696900
X-RAY DIFFRACTIONf_dihedral_angle_d13.6041817
X-RAY DIFFRACTIONf_chiral_restr0.06714
X-RAY DIFFRACTIONf_plane_restr0.003905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0592-3.22050.33871410.2782583X-RAY DIFFRACTION100
3.2205-3.42220.24881640.2172593X-RAY DIFFRACTION100
3.4222-3.68640.26341070.20322608X-RAY DIFFRACTION98
3.6864-4.05740.24611390.20182644X-RAY DIFFRACTION100
4.0574-4.64430.19211670.16222598X-RAY DIFFRACTION98
4.6443-5.85050.20211480.16512654X-RAY DIFFRACTION98
5.8505-59.9060.21731370.20212872X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0660.0440.62961.2499-0.05823.1631-0.071-0.16850.13870.20680.1181-0.0664-0.29960.5525-0.03550.8516-0.41740.00350.40650.02510.504965.964315.972169.2462
23.1909-2.03960.39623.5045-3.41055.0370.54840.55-0.2035-0.2408-0.3196-0.4745-0.15150.3715-0.05431.4081-0.4999-0.05490.856-0.18480.832474.168526.995791.5769
31.2552-0.3085-1.11552.3057-0.83271.9066-0.49620.02950.0398-0.18650.5869-0.2721-0.84290.5654-0.36410.9713-0.3644-0.11710.5789-0.18450.713872.272321.69893.6755
40.50670.0207-0.81120.0058-0.03431.27250.31640.65821.0053-0.01180.453-0.4068-0.27111.1-0.18891.1213-0.3221-0.0111.1396-0.04871.051478.980831.800296.4321
52.2007-0.10872.00361.71320.19554.85180.028-0.0729-0.4210.16710.076-0.02030.5340.0698-0.10440.6766-0.15650.00170.31610.04860.414265.9297-7.975272.523
61.2624-0.3356-1.41980.73991.39232.5524-0.3811-0.56360.2916-0.12770.439-0.0417-0.65610.5495-0.04110.647-0.0794-0.18540.4669-0.02990.485966.62659.600193.3128
76.9551.8056-3.05124.2432-0.85645.43310.04360.0024-0.3177-0.4524-0.0536-1.6075-0.09510.82280.10660.5436-0.12820.03120.8475-0.02340.707781.1387.448391.462
83.8504-0.0072-1.42431.1625-0.02583.2456-0.2862-0.8138-0.28730.2110.1248-0.06950.03850.95020.12110.55360.0961-0.09790.60350.09870.367164.86476.6865101.8023
93.99890.64670.5762.8193-0.90722.882-0.11560.6939-0.452-0.65650.2385-0.4991-0.00870.56570.0330.8509-0.2790.24640.6785-0.21620.55659.0363-12.710737.2865
102.90881.0149-0.17722.1266-0.01652.3947-0.21150.3522-0.0242-0.26740.2038-0.0102-0.21450.0245-0.01510.6639-0.26440.02120.4123-0.01130.446950.1306-5.094447.6929
114.3896-0.5744-0.63344.45641.1021.3024-0.5760.51810.4636-0.220.0577-0.1931-0.49620.15530.04680.7629-0.3312-0.02770.42010.03030.451155.37275.563846.8169
123.9754-0.68680.37714.41790.24651.24060.01450.1834-0.2303-0.32580.2386-1.548-0.62350.71040.05281.2683-0.59930.22080.8454-0.0430.552863.88362.547932.1849
131.1558-0.6443-1.12350.57420.04382.40040.1364-0.01940.2549-0.30780.2371-0.17740.74550.47130.10750.7376-0.30370.01210.4873-0.06340.53656.8529-3.378549.6437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 133 )
2X-RAY DIFFRACTION2chain 'C' and (resid 134 through 149 )
3X-RAY DIFFRACTION3chain 'C' and (resid 150 through 184 )
4X-RAY DIFFRACTION4chain 'C' and (resid 185 through 200 )
5X-RAY DIFFRACTION5chain 'D' and (resid 3 through 96 )
6X-RAY DIFFRACTION6chain 'D' and (resid 97 through 169 )
7X-RAY DIFFRACTION7chain 'D' and (resid 170 through 186 )
8X-RAY DIFFRACTION8chain 'D' and (resid 187 through 241 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 56 )
10X-RAY DIFFRACTION10chain 'A' and (resid 57 through 150 )
11X-RAY DIFFRACTION11chain 'A' and (resid 151 through 162 )
12X-RAY DIFFRACTION12chain 'A' and (resid 163 through 175 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 9 )

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