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- PDB-3qul: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 3qul
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4S)
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsIMMUNE SYSTEM / Murine MHC / LCMV / receptor binding / beta2-microglobulin / T cell recognition / T cell receptor / cell surface
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 Å
AuthorsAllerbring, E. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Grimm, S. / Tomek, M.B. / Mazumdar, P.A. / Spetz, A. / Friemann, R. / Sandalova, T. ...Allerbring, E. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Grimm, S. / Tomek, M.B. / Mazumdar, P.A. / Spetz, A. / Friemann, R. / Sandalova, T. / Uhlin, M. / Nygren, P. / Achour, A.
CitationJournal: Eur.J.Immunol. / Year: 2012
Title: Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics.
Authors: Allerbring, E.B. / Duru, A.D. / Uchtenhagen, H. / Madhurantakam, C. / Tomek, M.B. / Grimm, S. / Mazumdar, P.A. / Friemann, R. / Uhlin, M. / Sandalova, T. / Nygren, P.A. / Achour, A.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2May 3, 2017Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 13, 2023Group: Data collection / Database references / 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
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

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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: Pre-glycoprotein polyprotein GP complex
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Pre-glycoprotein polyprotein GP complex
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Pre-glycoprotein polyprotein GP complex
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)179,04512
Polymers179,04512
Non-polymers00
Water16,484915
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-15 kcal/mol
Surface area19270 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-17 kcal/mol
Surface area19370 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-21 kcal/mol
Surface area19640 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-19 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.041, 122.697, 99.123
Angle α, β, γ (deg.)90.00, 103.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
31H
41K
12A
22D
32G
42J

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
11ILEILEMETMET5BB1 - 991 - 99
21ILEILEMETMET5EE1 - 991 - 99
31ILEILEMETMET5HH1 - 991 - 99
41ILEILEMETMET5KK1 - 991 - 99
12GLYGLYGLUGLU4AA1 - 2751 - 275
22GLYGLYGLUGLU4DD1 - 2751 - 275
32GLYGLYGLUGLU4GG1 - 2751 - 275
42GLYGLYGLUGLU4JJ1 - 2751 - 275

NCS ensembles :
ID
1
2

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Components

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


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: UNP Residues 25-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / 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.: 4 / 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
#3: Protein/peptide
Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 969.135 Da / Num. of mol.: 4 / Fragment: UNP Residues 33-41 / Mutation: Y4S, C9M / Source method: obtained synthetically / Details: This sequence occurs naturally in LCMV / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 3.04 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.8 M ammonium sulfate, 0.1 M Tris HCl pH 9.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9395 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2→96.7 Å / Num. all: 150031 / Num. obs: 150031 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 3.9 / Num. unique all: 19978 / Rsym value: 0.327 / % possible all: 56.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SU7

1su7


Resolution: 2→51.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.009 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 7177 5 %RANDOM
Rwork0.20762 ---
obs0.20898 135615 98.92 %-
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: 32.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.01 Å2
2--0.26 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12305 0 0 915 13220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02113013
X-RAY DIFFRACTIONr_bond_other_d0.0010.029039
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.93717698
X-RAY DIFFRACTIONr_angle_other_deg0.809321816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93751540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61923.343673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.485152166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.28615106
X-RAY DIFFRACTIONr_chiral_restr0.0780.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022806
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_it0.7541.57674
X-RAY DIFFRACTIONr_mcbond_other0.1431.53047
X-RAY DIFFRACTIONr_mcangle_it1.438212435
X-RAY DIFFRACTIONr_scbond_it1.80335339
X-RAY DIFFRACTIONr_scangle_it3.0244.55263
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
11B528MEDIUM POSITIONAL0.280.5
12E528MEDIUM POSITIONAL0.30.5
13H528MEDIUM POSITIONAL0.160.5
14K528MEDIUM POSITIONAL0.170.5
11B751LOOSE POSITIONAL0.615
12E751LOOSE POSITIONAL0.75
13H751LOOSE POSITIONAL0.545
14K751LOOSE POSITIONAL0.535
11B528MEDIUM THERMAL1.412
12E528MEDIUM THERMAL2.832
13H528MEDIUM THERMAL1.632
14K528MEDIUM THERMAL3.292
11B751LOOSE THERMAL1.5410
12E751LOOSE THERMAL2.7410
13H751LOOSE THERMAL1.7210
14K751LOOSE THERMAL3.1710
21A3445MEDIUM POSITIONAL0.540.5
22D3445MEDIUM POSITIONAL0.620.5
23G3445MEDIUM POSITIONAL0.390.5
24J3445MEDIUM POSITIONAL0.430.5
21A3445MEDIUM THERMAL0.782
22D3445MEDIUM THERMAL0.782
23G3445MEDIUM THERMAL0.412
24J3445MEDIUM THERMAL0.392
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 521 -
Rwork0.258 10111 -
obs--99.63 %

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