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- PDB-1ffp: CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE ... -

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Basic information

Entry
Database: PDB / ID: 1ffp
TitleCRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE GP33 (C9M/K1S)
Components
  • BETA-2 MICROGLOBULIN BETA CHAIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B, ALPHA CHAIN
  • SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET
KeywordsIMMUNE SYSTEM/SIGNALING PROTEIN / major histocompatibility complex / peptide binding / T cell receptor / IMMUNE SYSTEM-SIGNALING PROTEIN 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 / 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: 2.6 Å
AuthorsWang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A.
Citation
Journal: J.IMMUNOL. / Year: 2002
Title: Peptidic termini play a significant role in TCR recognition
Authors: Wang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A.
#1: Journal: J.EXP.MED. / Year: 1999
Title: Structural evidence of T cell Xeno reactivity in the absence of molecular mimicry
Authors: Zhao, R. / Loftus, D.J. / Apella, E. / Collins, E.J.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 BETA CHAIN
C: SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET
D: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B, ALPHA CHAIN
E: BETA-2 MICROGLOBULIN BETA CHAIN
F: SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Theoretical massNumber of molelcules
Total (without water)89,2866
Polymers89,2866
Non-polymers00
Water25214
1
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B, ALPHA CHAIN
B: BETA-2 MICROGLOBULIN BETA CHAIN
C: SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Theoretical massNumber of molelcules
Total (without water)44,6433
Polymers44,6433
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area18610 Å2
MethodPISA
2
D: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B, ALPHA CHAIN
E: BETA-2 MICROGLOBULIN BETA CHAIN
F: SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Theoretical massNumber of molelcules
Total (without water)44,6433
Polymers44,6433
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-21 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.013, 66.897, 80.414
Angle α, β, γ (deg.)75.10, 72.90, 69.28
Int Tables number1
Space group name H-MP1
DetailsH-2Db heavy chain is noncovalently associated to Beat-2 microglobulin light chain. Heavy chain comprises of three subunits alpha1, alpha2 and alpha3. Peptide bind in the binding cleft formed by the alpha1 and alpha2 domains of heavy chain.

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Components

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


Mass: 31804.420 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01899
#2: Protein BETA-2 MICROGLOBULIN BETA CHAIN


Mass: 11835.555 Da / Num. of mol.: 2 / Fragment: BETA-2 MICROGLOBULIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide SYNTHETIC PEPTIDE WITH SEQUENCE SER-ALA-VAL-TYR-ASN-PHE-ALA-THR-MET


Mass: 1003.130 Da / Num. of mol.: 2 / Mutation: C9M/K1A / Source method: obtained synthetically / Details: The peptide was synthesized
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 8000, 6% DMSO, 0.8M Glycine, 150mM NaCl 25mM MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMMES1droppH6.5
310-20 %PEG80001reservoir
425 mMMES1reservoirpH6.5
51 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 25600 / Num. obs: 25600 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.01
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.025 / Num. unique all: 4107 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 109795
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.48

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.6→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 885473.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood function
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1304 5.1 %RANDOM
Rwork0.25 ---
all-25600 --
obs-25600 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.29 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-2.9 Å2-2.14 Å2
2--3.71 Å2-0.37 Å2
3----1.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 0 14 6302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 188 4.6 %
Rwork0.324 3919 -
obs--93.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Highest resolution: 2.6 Å

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