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- PDB-4h1l: TCR interaction with peptide mimics of nickel offers structural i... -

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Basic information

Entry
Database: PDB / ID: 4h1l
TitleTCR interaction with peptide mimics of nickel offers structural insights in nickel contact allergy
Components
  • Ani2.3 TCR A chain
  • Ani2.3 TCR B chain
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
  • mimotope peptide
KeywordsIMMUNE SYSTEM / PROTEIN-PROTEIN COMPLEX / immunoglobin fold / TCR recogniton of MHC / MHC II / glycosidation / membrane
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / early endosome membrane / adaptive immune response / cell surface receptor signaling pathway / lysosome / endosome membrane / immune response / Golgi membrane / lysosomal membrane / cell surface / signal transduction / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / : / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain ...: / : / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Immunoglobulin V-Type / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II antigen / Ani2.3 TCR A chain / Ani2.3 TCR B chain / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DR beta 3 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKappler, J.W. / Yin, L. / Dai, S. / Marrack, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: T-cell receptor (TCR) interaction with peptides that mimic nickel offers insight into nickel contact allergy.
Authors: Yin, L. / Crawford, F. / Marrack, P. / Kappler, J.W. / Dai, S.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: mimotope peptide
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
F: mimotope peptide
G: Ani2.3 TCR A chain
H: Ani2.3 TCR B chain
I: Ani2.3 TCR A chain
J: Ani2.3 TCR B chain


Theoretical massNumber of molelcules
Total (without water)138,35310
Polymers138,35310
Non-polymers00
Water00
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: mimotope peptide
I: Ani2.3 TCR A chain
J: Ani2.3 TCR B chain


Theoretical massNumber of molelcules
Total (without water)69,1775
Polymers69,1775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: MHC class II antigen
F: mimotope peptide
G: Ani2.3 TCR A chain
H: Ani2.3 TCR B chain


Theoretical massNumber of molelcules
Total (without water)69,1775
Polymers69,1775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.722, 186.722, 166.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 4:105 or resseq 114:190 )
211chain E and (resseq 4:105 or resseq 114:190 )
112chain A and (resseq 3:180 )
212chain D and (resseq 3:180 )
113chain G and (resseq 1:113 )
213chain I and (resseq 1:113 )
114chain H and (resseq 1:111 )
214chain J and (resseq 1:111 )
115chain C and (resseq -1:11 )
215chain F and (resseq -1:11 )

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 20727.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: baculovirus / Production host: HOMO SAPIENS (human) / References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 21848.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB3 / Plasmid: baculovirus / Production host: HOMO SAPIENS (human) / References: UniProt: D0AB36, UniProt: P79483*PLUS
#3: Protein/peptide mimotope peptide


Mass: 1539.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Antibody Ani2.3 TCR A chain


Mass: 12426.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: L7MTK9*PLUS
#5: Protein Ani2.3 TCR B chain


Mass: 12634.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: L7MTL0*PLUS
Has protein modificationY
Sequence detailsTHESE MISMATCHES ARE CONSEQUENCE OF A GENE RARE ALLELE OF HUMAN DR GENE (DR52C)

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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: 6.15 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Ammonium tartrate dibasic, 12% PEG 3350 , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 50237 / Num. obs: 46186 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_629)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.826 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 30.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 2346 4.37 %RANDOM
Rwork0.2633 ---
obs0.2643 44267 87.93 %-
all-50343 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.192 Å2 / ksol: 0.241 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.0564 Å2-0 Å2-0 Å2
2--12.0564 Å20 Å2
3----24.1129 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9630 0 0 0 9630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139894
X-RAY DIFFRACTIONf_angle_d1.50213408
X-RAY DIFFRACTIONf_dihedral_angle_d20.0123602
X-RAY DIFFRACTIONf_chiral_restr0.0921426
X-RAY DIFFRACTIONf_plane_restr0.0061750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1475X-RAY DIFFRACTIONPOSITIONAL
12E1475X-RAY DIFFRACTIONPOSITIONAL0.045
21A1465X-RAY DIFFRACTIONPOSITIONAL
22D1465X-RAY DIFFRACTIONPOSITIONAL0.069
31G878X-RAY DIFFRACTIONPOSITIONAL
32I878X-RAY DIFFRACTIONPOSITIONAL0.085
41H890X-RAY DIFFRACTIONPOSITIONAL
42J890X-RAY DIFFRACTIONPOSITIONAL0.075
51C107X-RAY DIFFRACTIONPOSITIONAL
52F107X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2791-3.36070.4314740.44071629X-RAY DIFFRACTION48
3.3607-3.45110.4281970.42982113X-RAY DIFFRACTION62
3.4511-3.55210.39171210.41442566X-RAY DIFFRACTION75
3.5521-3.66610.41381460.39172977X-RAY DIFFRACTION87
3.6661-3.79620.3751400.35733096X-RAY DIFFRACTION90
3.7962-3.94710.34631410.33373126X-RAY DIFFRACTION92
3.9471-4.12520.31881410.28453154X-RAY DIFFRACTION92
4.1252-4.34050.23821470.25593283X-RAY DIFFRACTION95
4.3405-4.60930.2631480.22743308X-RAY DIFFRACTION96
4.6093-4.960.23761540.20723334X-RAY DIFFRACTION98
4.96-5.44970.22171560.21053401X-RAY DIFFRACTION98
5.4497-6.21690.23181530.21363415X-RAY DIFFRACTION99
6.2169-7.7540.25231590.21033438X-RAY DIFFRACTION99
7.754-19.82640.24631570.213493X-RAY DIFFRACTION100

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