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- PDB-3tie: Crystal structure of the vaccinia derived peptide A11R in complex... -

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Basic information

Entry
Database: PDB / ID: 3tie
TitleCrystal structure of the vaccinia derived peptide A11R in complex with the murine MHC CLASS I H-2 KB
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Vaccinia derived octamer peptide
KeywordsIMMUNE SYSTEM / Antigen presentation / Peptide binding / IgG / MHC
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / beta-2-microglobulin binding / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / beta-2-microglobulin binding / Neutrophil degranulation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / defense response to bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Poxvirus A11 / Poxvirus A11 Protein / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Poxvirus A11 / Poxvirus A11 Protein / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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
H-2 class I histocompatibility antigen, K-B alpha chain / Beta-2-microglobulin / Protein A11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Vaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNguyen, T.T. / Shen, Z.T. / Stern, L.J.
CitationJournal: J.Immunol. / Year: 2013
Title: Disparate epitopes mediating protective heterologous immunity to unrelated viruses share peptide-MHC structural features recognized by cross-reactive T cells.
Authors: Shen, Z.T. / Nguyen, T.T. / Daniels, K.A. / Welsh, R.M. / Stern, L.J.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
C: Vaccinia derived octamer peptide
F: Vaccinia derived octamer peptide


Theoretical massNumber of molelcules
Total (without water)91,1286
Polymers91,1286
Non-polymers00
Water7,422412
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Vaccinia derived octamer peptide


Theoretical massNumber of molelcules
Total (without water)45,5643
Polymers45,5643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-14 kcal/mol
Surface area19770 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Vaccinia derived octamer peptide


Theoretical massNumber of molelcules
Total (without water)45,5643
Polymers45,5643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-13 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.264, 84.710, 87.895
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and ((resseq 1:160))
211chain 'D' and ((resseq 1:160))
112chain 'A' and ((resseq 230:277))
212chain 'D' and ((resseq 230:277))
113chain 'B'
213chain 'E'
114chain 'C'
214chain 'F'

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 32938.805 Da / Num. of mol.: 2 / Fragment: UNP residues 22-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Vaccinia derived octamer peptide


Mass: 876.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus / References: UniProt: Q49PI7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8K, Cacodylate, Magnesium Acetate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.089 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2010 / Details: Insertion Device
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.089 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 47727 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→43.507 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 22.64 / Stereochemistry target values: ML
Details: : statistics at the very beginning when nothing is done yet : 0.3125 0.3272 5.644575e+00 5.741753e+00 : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 : 32.545 0.7388 0.8882 24356.079 : 1. ...Details: : statistics at the very beginning when nothing is done yet : 0.3125 0.3272 5.644575e+00 5.741753e+00 : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 : 32.545 0.7388 0.8882 24356.079 : 1.174 0.009 0.082 13.097 0.004 4.121 9.0416e-02 : 12.018 0.084 0.439 84.894 0.024 2.029 5.7777e-02 : 135.06 10.02 35.57 135.06 11.04 35.90 58.45 10.02 30.53 : 0.000 0.000 0.000
RfactorNum. reflection% reflection
Rfree0.2193 2416 5.07 %
Rwork0.1823 --
obs0.1842 47665 99.57 %
all-47871 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.716 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8448 Å20 Å21.8433 Å2
2--10.8342 Å20 Å2
3----5.9894 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 0 412 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096507
X-RAY DIFFRACTIONf_angle_d1.1788829
X-RAY DIFFRACTIONf_dihedral_angle_d13.1142415
X-RAY DIFFRACTIONf_chiral_restr0.082909
X-RAY DIFFRACTIONf_plane_restr0.0041152
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1298X-RAY DIFFRACTIONPOSITIONAL0.043
12D1298X-RAY DIFFRACTIONPOSITIONAL0.043
21A388X-RAY DIFFRACTIONPOSITIONAL0.244
22D388X-RAY DIFFRACTIONPOSITIONAL0.244
31B855X-RAY DIFFRACTIONPOSITIONAL2.553
32E855X-RAY DIFFRACTIONPOSITIONAL2.553
41C61X-RAY DIFFRACTIONPOSITIONAL0.036
42F61X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33040.28842280.2254489X-RAY DIFFRACTION99
2.3304-2.42370.27662540.21644471X-RAY DIFFRACTION99
2.4237-2.5340.26882280.20944518X-RAY DIFFRACTION99
2.534-2.66760.29282190.21354532X-RAY DIFFRACTION100
2.6676-2.83470.25632370.20344508X-RAY DIFFRACTION100
2.8347-3.05350.26012480.18874523X-RAY DIFFRACTION100
3.0535-3.36070.2382430.20064514X-RAY DIFFRACTION100
3.3607-3.84680.20682540.18324554X-RAY DIFFRACTION100
3.8468-4.84550.15792510.13444543X-RAY DIFFRACTION100
4.8455-43.51470.18632540.17064597X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6684-0.0768-0.13250.84760.16570.8826-0.02170.01730.0784-0.03050.1474-0.24350.04920.0863-0.06420.08120.0020.02080.0727-0.02290.145517.5494-12.85631.008
20.87780.56670.10521.58921.01021.6080.06360.26370.1653-0.1731-0.45240.32660.0584-0.68130.28620.12540.05-0.06110.4047-0.09570.1522-18.5344-22.158524.2121
30.68-0.294-0.47540.23940.19650.32970.0199-0.02020.08940.02280.02260.0733-0.0138-0.0066-0.03390.052-0.0122-0.00270.03490.00140.0505-7.676-16.838744.0457
40.23990.1943-0.00010.2534-0.12420.22420.00940.19180.09520.0388-0.0449-0.15830.03020.157-0.02070.10940.00230.0420.211-0.02110.276723.294-9.97231.3303
50.5609-0.1491-0.14610.73640.0810.94320.0017-0.1767-0.0294-0.00390.02390.0788-0.0245-0.1187-0.01210.11450.0189-0.00110.1157-0.01680.0745-8.5533-15.5745-8.6211
61.0364-0.1768-0.12270.789-0.63981.3895-0.0053-0.24730.17280.0523-0.229-0.15560.13180.49630.18510.0948-0.0114-0.05310.26940.0610.092627.5809-24.7388-0.2453
70.6579-0.16640.21321.1634-0.2410.290.10740.15710.0488-0.1006-0.1321-0.12950.05720.09-0.09840.1250.06140.00450.11380.00090.077916.4987-22.2608-20.3453
80.26240.1310.36370.06790.2070.58990.0978-0.04290.0708-0.00680.1464-0.00720.0336-0.2068-0.19220.07770.07420.03890.25210.01910.2043-14.549-12.737-9.7589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:180)
2X-RAY DIFFRACTION2chain 'A' and (resseq 181:277)
3X-RAY DIFFRACTION3chain 'B'
4X-RAY DIFFRACTION4chain 'C'
5X-RAY DIFFRACTION5chain 'D' and (resseq 1:180)
6X-RAY DIFFRACTION6chain 'D' and (resseq 181:277)
7X-RAY DIFFRACTION7chain 'E'
8X-RAY DIFFRACTION8chain 'F'

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