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- PDB-7p0t: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ... -

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Basic information

Entry
Database: PDB / ID: 7p0t
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH LCMV-DERIVED GP33 PEPTIDE with D-AMINOACID
Components
  • Beta-2-microglobulin
  • Derived peptide gp33-41 from LCMV
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / D-aminoacid / class I major histocompatibility complex / b2-microglobulin
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 / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / 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 / 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 / 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 / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å
AuthorsBroggini, L. / Ricagno, S.
CitationJournal: Acs Omega / Year: 2022
Title: l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics.
Authors: Ballabio, F. / Broggini, L. / Paissoni, C. / Han, X. / Peqini, K. / Sala, B.M. / Sun, R. / Sandalova, T. / Barbiroli, A. / Achour, A. / Pellegrino, S. / Ricagno, S. / Camilloni, C.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Derived peptide gp33-41 from LCMV
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Derived peptide gp33-41 from LCMV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,85515
Polymers90,0516
Non-polymers8049
Water1,31573
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Derived peptide gp33-41 from LCMV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5419
Polymers45,0263
Non-polymers5166
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-87 kcal/mol
Surface area17470 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Derived peptide gp33-41 from LCMV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3146
Polymers45,0263
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-56 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.512, 124.602, 92.915
Angle α, β, γ (deg.)90.00, 126.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11892.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Derived peptide gp33-41 from LCMV


Mass: 1045.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis mammarenavirus
Production host: synthetic construct (others)

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Non-polymers , 3 types, 82 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 60.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.7 M Ammonium Sulphate, 100 mM Tris-HCl, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.2 Å / Num. obs: 22227 / % possible obs: 92 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 16.1
Reflection shellResolution: 2.605→2.893 Å / Num. unique obs: 1309 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.605→48.2 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2017 9.08 %
Rwork0.1974 --
obs0.2017 22225 66.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.605→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 41 73 5683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055797
X-RAY DIFFRACTIONf_angle_d0.7687922
X-RAY DIFFRACTIONf_dihedral_angle_d7.3333756
X-RAY DIFFRACTIONf_chiral_restr0.047818
X-RAY DIFFRACTIONf_plane_restr0.0051025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.605-2.67010.4841110.423993X-RAY DIFFRACTION4
2.6701-2.74230.5838250.3944212X-RAY DIFFRACTION10
2.7423-2.8230.4367450.3763398X-RAY DIFFRACTION19
2.823-2.91410.4446610.3327629X-RAY DIFFRACTION29
2.9141-3.01820.3218800.2989972X-RAY DIFFRACTION44
3.0182-3.1390.28471370.26811252X-RAY DIFFRACTION58
3.139-3.28190.35121570.251541X-RAY DIFFRACTION71
3.2819-3.45480.30162060.23742006X-RAY DIFFRACTION91
3.4548-3.67120.2332110.21822149X-RAY DIFFRACTION100
3.6712-3.95460.22262110.18322175X-RAY DIFFRACTION100
3.9546-4.35230.23842130.16222188X-RAY DIFFRACTION100
4.3523-4.98150.20552240.14742174X-RAY DIFFRACTION100
4.9815-6.2740.22752100.19042211X-RAY DIFFRACTION100
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)
15.61460.0375-1.44562.54510.2113.83160.1006-0.5439-0.32230.6293-0.03960.46780.081-0.62080.06740.3316-0.01670.13010.2860.07890.3376-20.6287-5.397212.1212
27.612-4.3566-3.56836.8154.39894.0491-0.0467-0.44851.49590.94680.391-0.1915-0.7976-0.42980.03090.71080.42340.20210.20380.03670.4366-19.399911.636811.734
32.7390.39021.03283.2688-0.05832.0317-0.29340.01130.7488-0.01030.17810.6646-0.9459-0.2955-0.01250.4430.1760.13920.04120.070.4833-17.45926.86913.1619
41.32330.184-1.82792.87850.39793.2533-0.414-2.21630.67271.82570.0918-0.3852-0.86660.01760.37351.9270.0163-0.07471.0795-0.07880.6944-9.60638.740.5556
55.35812.04870.38924.91620.65165.13050.0014-0.63351.44721.0550.1298-0.4159-1.50670.2513-0.18461.13670.0238-0.18710.7759-0.15640.8092-7.370611.267537.205
64.6046-0.3098-3.83852.71720.31693.2036-0.3395-0.91510.21190.02640.22080.29330.02142.04930.18340.430.0366-0.0040.97820.26860.4285-1.6831-4.693225.9202
72.51191.38520.27474.9136-2.07251.2215-0.2224-1.4277-0.19761.6503-0.14430.2663-0.56920.66520.0860.84180.12290.0151.11780.10460.3744-10.567-3.725840.8584
80.264-0.75320.55663.2173-2.97828.5564-0.1019-0.994-0.79190.63970.37340.62080.2049-0.1456-0.13020.47810.17960.00960.68450.37380.4423-8.9698-9.192124.9352
93.4021-0.7130.05713.4091-1.51990.6956-0.0445-1.4869-0.10120.7640.2208-0.40870.56930.7475-0.08020.68830.4577-0.05511.36160.36910.4484-3.4757-11.075735.2451
105.8246-3.1492-4.72754.315.12936.3757-0.186-0.2106-0.1679-0.2778-0.10080.82130.7271-0.86830.02530.27890.12080.02220.34220.22260.5071-22.9057-0.49722.4498
118.28060.7046-2.6016.05031.4587.8250.1085-1.51460.2520.7529-0.1322-0.1112-0.6257-0.21570.1590.58320.0628-0.03010.942-0.10040.4979-13.000647.148425.2727
122.530.1801-2.58662.7110.48195.86810.1593-1.10730.49810.6507-0.0804-0.2362-0.32390.652-0.11240.48190.0054-0.29631.0193-0.13450.5144-2.563647.88618.6909
130.36880.69930.03915.2426-1.45454.562-0.092-0.8343-0.71320.4064-0.4206-1.03150.99370.82250.33090.61340.1665-0.1311.03690.29660.6831-1.487134.723318.0225
144.4234-0.1352-0.60644.45111.32250.4634-0.8460.092-0.5243-0.1921-0.50712.3126-1.1567-0.0830.42940.9277-0.0553-0.3380.8340.21351.8952-41.499933.137312.8181
156.29913.84061.72363.69553.3857.731-0.30290.5263-0.7991-0.79520.66891.83360.67490.92610.16560.99440.119-0.25110.47870.04051.2416-34.583433.254211.9825
163.4619-0.0835-0.3471.10481.43341.867-0.3136-0.0073-0.9786-0.1946-0.09752.22960.8505-0.76580.30081.1865-0.0573-0.0610.338-0.01661.8457-38.956926.735711.7212
173.6214-3.7423-3.6197.73870.55636.22020.24630.1714-0.8412-0.23-0.0622-0.3870.05630.2472-0.03770.26610.0685-0.14480.3967-0.00190.4562-25.375146.87996.4736
182.0950.6254-2.31350.6185-0.24353.0045-0.6302-1.8832-1.85240.70460.68290.8366-0.024-0.220.29260.26540.18410.21720.93810.41650.8722-37.936946.668917.5293
193.8047-0.2213-4.26316.07041.47215.2650.47380.03840.65980.1484-0.4278-0.9073-0.14770.29260.19180.2387-0.0054-0.15460.4823-0.13070.3366-23.811453.93629.9933
202.9026-3.27320.42173.6774-0.47220.0608-0.8558-1.77940.75950.78770.7194-0.9123-0.47060.3022-0.03070.67530.1706-0.20031.0563-0.160.5511-28.14255.25416.976
212.0003-2.814-1.3762.2944-0.4780.67350.0019-0.2579-1.4683-0.2809-0.1008-0.11250.6257-0.10910.10680.29480.0505-0.18170.7650.04340.8711-15.587142.09211.4456
220.03830.3179-0.04982.6317-0.30352.6919-0.4892-2.933-0.69870.90340.74270.6099-0.1491-1.1856-0.21210.3990.15360.04890.98530.14080.3656-39.230452.663316.3376
232.25920.46911.86081.38590.96557.75961.02630.2817-0.52880.5233-0.1058-0.1398-0.5672-0.0288-0.69770.53310.2427-0.06370.35750.05470.3431-32.771755.65868.9318
246.9114-5.8162-3.60225.4122.2563.44870.00952.77492.4723-0.5279-0.5881-1.4586-1.7712-1.01040.30470.76840.051-0.10721.10950.17591.0545-21.946256.60581.1488
256.3386-0.101-6.32365.709-0.22186.3279-0.9570.491-2.0428-0.04030.31560.28840.91810.19850.09360.42410.2824-0.14310.5491-0.12270.6663-38.563448.66877.1417
263.70472.4903-3.70293.97-4.40665.31.09870.0340.7021.5779-0.2502-0.5962-0.59840.5342-0.85211.26-0.1062-0.32611.54390.0760.6571.531742.886523.217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 273 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 99 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 9 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 56 )
12X-RAY DIFFRACTION12chain 'D' and (resid 57 through 103 )
13X-RAY DIFFRACTION13chain 'D' and (resid 104 through 173 )
14X-RAY DIFFRACTION14chain 'D' and (resid 174 through 197 )
15X-RAY DIFFRACTION15chain 'D' and (resid 198 through 240 )
16X-RAY DIFFRACTION16chain 'D' and (resid 241 through 274 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 11 )
18X-RAY DIFFRACTION18chain 'E' and (resid 12 through 28 )
19X-RAY DIFFRACTION19chain 'E' and (resid 29 through 41 )
20X-RAY DIFFRACTION20chain 'E' and (resid 42 through 56 )
21X-RAY DIFFRACTION21chain 'E' and (resid 57 through 63 )
22X-RAY DIFFRACTION22chain 'E' and (resid 64 through 77 )
23X-RAY DIFFRACTION23chain 'E' and (resid 78 through 83 )
24X-RAY DIFFRACTION24chain 'E' and (resid 84 through 90 )
25X-RAY DIFFRACTION25chain 'E' and (resid 91 through 99 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 9 )

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