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- PDB-3tbv: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ... -

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Basic information

Entry
Database: PDB / ID: 3tbv
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (A2G,V3P,Y4A)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Glycoprotein G1
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsImmune system/agonist / Murine MHC / LCMV / receptor binding / Beta2-microglobulin / Immune system / T cell recognition / antigen presentation / altered peptide ligand / agonism / antagonism / T cell receptor / CD8 / Cell Surface / Immune system-agonist complex
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / 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 ...TAP1 binding / TAP2 binding / 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 / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / host cell Golgi membrane / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / receptor-mediated endocytosis of virus by host cell
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDuru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.
CitationJournal: To be Published
Title: Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition
Authors: Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Glycoprotein G1
J: Glycoprotein G1
K: Glycoprotein G1
L: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,94623
Polymers178,91712
Non-polymers1,02911
Water16,033890
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
I: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1027
Polymers44,7293
Non-polymers3724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-19 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
J: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8254
Polymers44,7293
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-19 kcal/mol
Surface area19520 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
K: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1057
Polymers44,7293
Non-polymers3764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-20 kcal/mol
Surface area19550 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
L: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9135
Polymers44,7293
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.584, 126.473, 102.110
Angle α, β, γ (deg.)90.00, 106.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H2-DB / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 4 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887

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Protein/peptide , 1 types, 4 molecules IJKL

#3: Protein/peptide
Glycoprotein G1


Mass: 937.094 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-41 / Mutation: A34G,V35P,Y36A / Source method: obtained synthetically / Details: LYMPHOCYTIC CHORIOMENINGITIS VIRUS GP1 / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399

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Non-polymers , 3 types, 901 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization ...Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: Bruker AXS/Roentec X-Flash XRF detector / Detector: X-Flash XRF detector / Date: Sep 9, 2009
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→74.7 Å / Num. all: 152694 / Num. obs: 152694 / % possible obs: 96.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / % possible all: 80

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.1→49.51 Å / SU ML: 0.4 / σ(F): 1.55 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 13353 5.02 %Random
Rwork0.2245 ---
all0.2272 266018 --
obs0.2272 -98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.326 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3056 Å20 Å23.4846 Å2
2--3.7892 Å2-0 Å2
3----4.0948 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12596 0 62 890 13548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213031
X-RAY DIFFRACTIONf_angle_d1.8617659
X-RAY DIFFRACTIONf_dihedral_angle_d21.1634746
X-RAY DIFFRACTIONf_chiral_restr0.1131772
X-RAY DIFFRACTIONf_plane_restr0.0112296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.343912850.288622762X-RAY DIFFRACTION89
2.1751-2.26210.455712120.414425274X-RAY DIFFRACTION98
2.2621-2.36510.375413300.29425328X-RAY DIFFRACTION99
2.3651-2.48980.317113340.241525717X-RAY DIFFRACTION100
2.4898-2.64580.301113280.235425618X-RAY DIFFRACTION100
2.6458-2.850.290814080.2225692X-RAY DIFFRACTION100
2.85-3.13680.275614230.212325476X-RAY DIFFRACTION100
3.1368-3.59060.270813630.208725674X-RAY DIFFRACTION100
3.5906-4.52330.209613300.163325661X-RAY DIFFRACTION100
4.5233-49.52380.21513400.173325463X-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)
11.27560.7856-1.13741.2413-0.85091.6905-0.36690.59220.0602-0.2520.44420.16190.3474-0.6473-0.07660.2495-0.1835-0.05870.35790.06050.148647.0961-1.897813.0445
21.33510.1542-0.47822.7119-0.74190.93560.05160.07850.04190.74350.10590.1365-0.1553-0.3978-0.12320.2464-0.06750.01260.21790.04560.227830.0729.262643.6322
30.50680.2422-0.79920.977-0.57541.4375-0.2130.1112-0.0625-0.0480.1283-0.06330.6075-0.36690.12160.2439-0.14880.02130.20650.00490.10236.3865-11.658137.5064
41.34170.4314-0.2780.5888-0.30390.45880.0692-0.1168-0.06750.0928-0.076-0.0794-0.1915-0.05970.02940.19760.05280.00070.09780.01820.118644.539539.741833.1876
50.83451.1514-0.72312.4903-1.25490.6613-0.3943-0.2563-0.5539-0.88860.43460.22160.5871-0.5972-0.06990.50460.0187-0.11410.4120.17280.527933.11128.17820.4242
60.3664-0.21830.77030.906-1.08582.05120.07710.0749-0.0530.020.28520.1198-0.3799-0.6289-0.26050.20280.14910.02370.30360.09230.088937.227649.27157.0508
71.9021-0.6933-0.73490.38540.31180.73850.10650.2072-0.0694-0.1547-0.08990.0881-0.29830.1353-0.01880.1802-0.0545-0.00020.1245-0.00350.1124-12.195140.520815.3926
80.2828-0.6629-0.11482.19981.26061.7293-0.4298-0.1099-0.29420.80560.75580.12160.69171.1232-0.23380.52420.2783-0.07030.5043-0.00670.24930.769330.053848.2281
90.5319-0.10670.24990.30340.18142.69080.0455-0.28450.06010.02910.1764-0.0401-0.56880.5914-0.14640.1917-0.13370.00670.2489-0.05470.0602-5.15850.874641.2213
101.4991-0.4219-0.70770.94220.23251.3264-0.2269-0.3284-0.00410.18460.1732-0.03410.37570.35120.02430.19650.1795-0.02570.1705-0.00620.0961-12.1256-0.629736.0351
111.67670.0593-0.09313.45890.19750.60110.00680.32990.0915-0.88050.1688-0.33820.06890.2668-0.01570.27210.13690.0610.2971-0.02170.19513.886510.65545.1845
120.5389-0.3562-0.57490.81530.63590.7315-0.22150.1584-0.20940.25150.13640.06650.51650.22690.07810.35210.18190.05490.2887-0.00070.1584-1.0209-10.44211.8057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:175)
2X-RAY DIFFRACTION2(chain A and resid 176:276)
3X-RAY DIFFRACTION3(chain B and resid 1:99)
4X-RAY DIFFRACTION4(chain C and resid 1:175)
5X-RAY DIFFRACTION5(chain C and resid 176:274)
6X-RAY DIFFRACTION6(chain D and resid 1:99)
7X-RAY DIFFRACTION7(chain E and resid 1:175)
8X-RAY DIFFRACTION8(chain E and resid 176:276)
9X-RAY DIFFRACTION9(chain F and resid 1:99)
10X-RAY DIFFRACTION10(chain G and resid 1:175)
11X-RAY DIFFRACTION11(chain G and resid 176:276)
12X-RAY DIFFRACTION12(chain H and resid 1:99)

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