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- PDB-1ed3: CRYSTAL STRUCTURE OF RAT MINOR HISTOCOMPATIBILITY ANTIGEN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1ed3
TitleCRYSTAL STRUCTURE OF RAT MINOR HISTOCOMPATIBILITY ANTIGEN COMPLEX RT1-AA/MTF-E.
Components
  • BETA-2-MICROGLOBULIN
  • CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
  • PEPTIDE MTF-E (13N3E)
KeywordsIMMUNE SYSTEM / major histocompatibility complex / rat minor histocompatibility complex / MHC / immunology / peptide antigen presentation / cellular immunity / cell surface receptor / T cell receptor ligand
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Mitochondrial protein degradation / DAP12 signaling / proton channel activity ...Formation of ATP by chemiosmotic coupling / Cristae formation / Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Mitochondrial protein degradation / DAP12 signaling / proton channel activity / Neutrophil degranulation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / 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 / response to hyperoxia / response to cadmium ion / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / MHC class II protein complex binding / late endosome membrane / 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 / mitochondrial inner membrane / immune response / response to xenobiotic stimulus / signaling receptor binding / lysosomal membrane / external side of plasma membrane / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding
Similarity search - Function
ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / 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 ...ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / 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
ATP synthase F(0) complex subunit a / Beta-2-microglobulin / RT1 class I histocompatibility antigen, AA alpha chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSpeir, J.A. / Stevens, J. / Joly, E. / Butcher, G.W. / Wilson, I.A.
Citation
Journal: Immunity / Year: 2001
Title: Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa.
Authors: Speir, J.A. / Stevens, J. / Joly, E. / Butcher, G.W. / Wilson, I.A.
#1: Journal: J.Immunol. / Year: 1997
Title: Identification of the rat maternally transmitted minor histocompatibility antigen
Authors: Bhuyan, P.K. / Young, L.L. / Lindahl, K.F. / Butcher, G.W.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: Efficient generation of major histocompatibility complex class I-peptide complexes using synthetic peptide libraries
Authors: Stevens, J. / Wiesmuller, K.-H. / Barker, P.J. / Walden, P. / Bucher, G.W. / Joly, E.
#3: Journal: Eur.J.Biochem. / Year: 1998
Title: Peptide length preferences for rat and mouse MHC class I molecules using random peptide libraries
Authors: Stevens, J. / Wiesmuller, K.-H. / Walden, P. / Joly, E.
#4: Journal: Immunity / Year: 1996
Title: The rat cim effect: TAP allele-dependent changes in a class I MHC anchor motif and evidence against C-terminal trimming of peptides in the ER
Authors: Powis, S.J. / Young, L.L. / Joly, E. / Barker, P.J. / Richardson, L. / Brandt, R.P. / Melief, C.J. / Howard, J.C. / Butcher, G.W.
#5: Journal: Immunogenetics / Year: 1995
Title: An analysis of the antigen binding site of RT1-Aa suggests an allele-specific motif
Authors: Thorpe, C.J. / Moss, D.S. / Powis, S.J. / Howard, J.C. / Butcher, G.W. / Travers, P.J.
History
DepositionJan 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
B: BETA-2-MICROGLOBULIN
C: PEPTIDE MTF-E (13N3E)
D: CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
E: BETA-2-MICROGLOBULIN
F: PEPTIDE MTF-E (13N3E)


Theoretical massNumber of molelcules
Total (without water)90,4636
Polymers90,4636
Non-polymers00
Water2,504139
1
A: CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
B: BETA-2-MICROGLOBULIN
C: PEPTIDE MTF-E (13N3E)


Theoretical massNumber of molelcules
Total (without water)45,2323
Polymers45,2323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-16 kcal/mol
Surface area19100 Å2
MethodPISA
2
D: CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA
E: BETA-2-MICROGLOBULIN
F: PEPTIDE MTF-E (13N3E)


Theoretical massNumber of molelcules
Total (without water)45,2323
Polymers45,2323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-17 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.95, 90.72, 117.41
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3
DetailsThere are two heterotrimeric biological assemblies in the asymmetric unit constructed from chains A, B, and C, or chains D, E, and F.

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Components

#1: Protein CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA


Mass: 32045.551 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / References: UniProt: P16391
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11652.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / References: UniProt: P07151
#3: Protein/peptide PEPTIDE MTF-E (13N3E)


Mass: 1533.773 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-41 OF RAT ATPASE 6 / Source method: obtained synthetically / Details: This sequence occurs naturally in rats / References: UniProt: P05504
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.46 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M morpholine ethansulfonic acid (MES), 0.2M ammonium sulfate, 15-20% MPEG 5000, 0.025M beta-octyl-glucoside, 0.5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMHEPES1drop
325 mM1dropNaCl
41 mMEDTA1drop
50.1 MMES1reservoir
60.2 Mammonium sulfate1reservoir
715-20 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 28978 / Num. obs: 28978 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.4
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2757 / % possible all: 91.2
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 91.2 % / Num. unique obs: 2757

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CLR

2clr


Resolution: 2.55→19.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Engh & Huber as implemented in X-PLOR and CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2177 7.5 %Random
Rwork0.222 ---
all-28993 --
obs-28978 93.9 %-
Solvent computationBsol: 33.8132 Å2 / ksol: 0.368077 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2---6.74 Å20 Å2
3---3.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.55→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 0 139 6519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg25.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.87
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.462.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINEDX-RAY DIFFRACTION0.04300
22RESTRAINEDX-RAY DIFFRACTION0.044300
33RESTRAINEDX-RAY DIFFRACTION0.039300
LS refinement shellResolution: 2.55→2.64 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 197 7.5 %
Rwork0.319 2414 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.319 / Rfactor obs: 0.319

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