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- PDB-1fg2: CRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE GP33 IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 1fg2
TitleCRYSTAL STRUCTURE OF THE LCMV PEPTIDIC EPITOPE GP33 IN COMPLEX WITH THE MURINE CLASS I MHC MOLECULE H-2DB
Components
  • BETA-2 MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
  • LCMV PEPTIDIC EPITOPE GP33
KeywordsIMMUNE SYSTEM / Ig Fold
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 / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...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 / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / 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-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 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.754 Å
AuthorsTissot, A.C. / Ciatto, C. / Mittl, P.R.E. / Gruetter, M.G. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex.
Authors: Tissot, A.C. / Ciatto, C. / Mittl, P.R. / Grutter, M.G. / Pluckthun, A.
History
DepositionJul 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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: LCMV PEPTIDIC EPITOPE GP33
D: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
E: BETA-2 MICROGLOBULIN
F: LCMV PEPTIDIC EPITOPE GP33
G: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
H: BETA-2 MICROGLOBULIN
I: LCMV PEPTIDIC EPITOPE GP33
J: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
K: BETA-2 MICROGLOBULIN
L: LCMV PEPTIDIC EPITOPE GP33


Theoretical massNumber of molelcules
Total (without water)181,81612
Polymers181,81612
Non-polymers00
Water2,018112
1
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
B: BETA-2 MICROGLOBULIN
C: LCMV PEPTIDIC EPITOPE GP33


Theoretical massNumber of molelcules
Total (without water)45,4543
Polymers45,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-19 kcal/mol
Surface area18840 Å2
MethodPISA
2
D: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
E: BETA-2 MICROGLOBULIN
F: LCMV PEPTIDIC EPITOPE GP33


Theoretical massNumber of molelcules
Total (without water)45,4543
Polymers45,4543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-19 kcal/mol
Surface area19020 Å2
MethodPISA
3
G: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
H: BETA-2 MICROGLOBULIN
I: LCMV PEPTIDIC EPITOPE GP33


Theoretical massNumber of molelcules
Total (without water)45,4543
Polymers45,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-19 kcal/mol
Surface area18970 Å2
MethodPISA
4
J: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
K: BETA-2 MICROGLOBULIN
L: LCMV PEPTIDIC EPITOPE GP33


Theoretical massNumber of molelcules
Total (without water)45,4543
Polymers45,4543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-20 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.527, 124.770, 99.555
Angle α, β, γ (deg.)90.00, 103.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN / H-2D(B)


Mass: 32601.303 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR ALPHA CHAIN (1,2,3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3) / References: UniProt: P01899
#2: Protein
BETA-2 MICROGLOBULIN


Mass: 11835.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3) / References: UniProt: P01887
#3: Protein/peptide
LCMV PEPTIDIC EPITOPE GP33


Mass: 1017.178 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, PEG 4000, hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.85 mg/mlprotein1drop
20.1 Mammonium sulfate1reservoir
320 %(w/v)PEG40001reservoir
40.1 MHEPES1reservoir
50.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→29.9 Å / Num. all: 51494 / Num. obs: 51494 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.75→2.81 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.386 / % possible all: 90.8
Reflection shell
*PLUS
% possible obs: 88.4 % / Num. unique obs: 3331 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.754→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 5197 random
Rwork0.236 --
all-51474 -
obs-51474 -
Refinement stepCycle: LAST / Resolution: 2.754→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12548 0 0 112 12660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_torsion_deg25.1
X-RAY DIFFRACTIONc_torsion_impr_deg0.89

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