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

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Basic information

Entry
Database: PDB / ID: 3tbs
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX THE WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P,Y4A)
Components
  • Beta-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


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 / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / host cell Golgi membrane / 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 / receptor-mediated endocytosis of virus by host cell / learning or memory / host cell endoplasmic reticulum membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
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: 2.49 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: GLYCOPROTEIN G1
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: GLYCOPROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,86310
Polymers89,4866
Non-polymers3764
Water2,648147
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: GLYCOPROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9315
Polymers44,7433
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-15 kcal/mol
Surface area19610 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: GLYCOPROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9315
Polymers44,7433
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-16 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.840, 125.120, 101.320
Angle α, β, γ (deg.)90.00, 128.15, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13B
23E
14A
24D
33B
44A

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU2AA1 - 1541 - 154
21GLYGLYGLUGLU2DD1 - 1541 - 154
12TYRTYRLYSLYS2AA156 - 173156 - 173
22TYRTYRLYSLYS2DD156 - 173156 - 173
13ILEILEMETMET1BB1 - 991 - 99
23ILEILEMETMET1EE1 - 991 - 99
14LEULEUARGARG2AA180 - 273180 - 273
24LEULEUARGARG2DD180 - 273180 - 273

NCS ensembles :
ID
1
2
3
4

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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 25-362
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


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: UNP 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, 2 molecules CF

#3: Protein/peptide GLYCOPROTEIN G1


Mass: 951.120 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-41 / Mutation: V35P,Y36A / Source method: obtained synthetically / Details: LYMPHOCYTIC CHORIOMENINGITIS VIRUS / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399

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Non-polymers , 3 types, 151 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
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: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.49→49.21 Å / Num. all: 40587 / Num. obs: 40587 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5927 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.49→49.21 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 23.066 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27044 2006 5 %RANDOM
Rwork0.22961 ---
all0.23164 38455 --
obs0.23164 38455 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.37 Å2
2---0.1 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.49→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 22 147 6389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216445
X-RAY DIFFRACTIONr_bond_other_d0.0030.024446
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.948751
X-RAY DIFFRACTIONr_angle_other_deg0.958310733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40823.554332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.157151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4451548
X-RAY DIFFRACTIONr_chiral_restr0.0760.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217167
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021367
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3181.53803
X-RAY DIFFRACTIONr_mcbond_other0.0931.51516
X-RAY DIFFRACTIONr_mcangle_it0.60126129
X-RAY DIFFRACTIONr_scbond_it1.03632642
X-RAY DIFFRACTIONr_scangle_it1.6224.52622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A903tight positional0.030.05
22A107tight positional0.020.05
33B1407tight positional0.050.05
44A532tight positional0.020.05
11A1287medium positional0.040.5
22A173medium positional0.020.5
44A690medium positional0.080.5
11A903tight thermal0.070.5
22A107tight thermal0.050.5
33B1407tight thermal0.080.5
44A532tight thermal0.040.5
11A1287medium thermal0.082
22A173medium thermal0.082
44A690medium thermal0.042
LS refinement shellResolution: 2.487→2.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 151 -
Rwork0.33 2770 -
obs--96.85 %
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)
11.58020.50690.66992.48461.16525.31580.009-0.2308-0.07110.2977-0.018-0.032-0.0458-0.05120.00890.04690.01580.00730.07370.04240.0498-23.6650-18.363
24.37560.9818-1.86146.3287-0.46952.9887-0.098-0.09970.6591-0.50380.2187-0.6583-0.55140.2097-0.12060.4048-0.0682-0.06060.2465-0.08420.4959.63411.095-26.114
310.0363-3.01670.20242.6471-0.08181.9123-0.1406-0.4013-0.13070.10170.1146-0.14850.16120.32050.0260.05030.0090.0030.10250.00390.02381.689-9.91-26.832
43.7867-0.61041.07983.8174-0.48523.30510.0523-0.2506-0.0390.44170.038-0.6016-0.13370.4692-0.09030.0988-0.0633-0.01750.1543-0.07230.1733-7.35940.886-30.276
53.44160.3346-1.1667.36510.79453.1054-0.2708-0.2744-0.30970.83320.07230.77550.6938-0.33170.19840.4217-0.04430.04990.2639-0.06640.3187-23.90130.0930.673
61.7383-0.2144-0.14442.19551.79738.63320.0308-0.16470.23290.0169-0.0193-0.2531-0.19240.2359-0.01140.0624-0.04990.01340.1131-0.07680.1659-20.7851.068-8.255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION2A174 - 275
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4D1 - 183
5X-RAY DIFFRACTION5D184 - 275
6X-RAY DIFFRACTION6E1 - 99

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