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- PDB-1kjm: TAP-A-associated rat MHC class I molecule -

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Basic information

Entry
Database: PDB / ID: 1kjm
TitleTAP-A-associated rat MHC class I molecule
Components
  • B6 Peptide
  • RT1 class I histocompatibility antigen, AA alpha chain, heavy chain
  • beta-2-Microglobulin
KeywordsIMMUNE SYSTEM / peptide-MHC complex / heterodimer / extracellular domain
Function / homology
Function and homology information


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 / DAP12 signaling / 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 / response to cadmium ion ...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 / DAP12 signaling / 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 / response to cadmium ion / 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 / 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
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 / RT1 class I histocompatibility antigen, AA alpha chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B.
Authors: Rudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A.
#1: 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.S. / Joly, E. / Butcher, G.W. / Wilson, I.A.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: 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: RT1 class I histocompatibility antigen, AA alpha chain, heavy chain
B: beta-2-Microglobulin
P: B6 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1314
Polymers46,0353
Non-polymers961
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.049, 109.566, 45.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

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Components

#1: Protein RT1 class I histocompatibility antigen, AA alpha chain, heavy chain / MHC class I RT1-AA heavy chain


Mass: 33326.961 Da / Num. of mol.: 1
Fragment: extracellular domain, residues 25-300, numbered 1-276, plus C-terminal his tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P16391
#2: Protein beta-2-Microglobulin


Mass: 11783.478 Da / Num. of mol.: 1 / Fragment: residues 21-119, numbered 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P07151
#3: Protein/peptide B6 Peptide


Mass: 924.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide was derived from biochemical binding data.
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
31 %(v/v)glycerol1reservoir
40.1 MTris-HCl1reservoirp8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→19.8 Å / Num. obs: 22313 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.76 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.38 % / Mean I/σ(I) obs: 1.86 / Num. unique all: 2120 / Rsym value: 0.423 / % possible all: 92
Reflection
*PLUS
Redundancy: 2.8 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92 % / Redundancy: 2.4 % / Num. unique obs: 2120 / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ED3 MOLECULE 1

1ed3


Resolution: 2.35→19.8 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.91 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26803 2156 10 %RANDOM
Rwork0.2473 ---
obs0.24935 21660 97.16 %-
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: 11.686 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--5.96 Å20 Å2
3----4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 5 144 3298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9414409
X-RAY DIFFRACTIONr_angle_other_deg0.78336547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0773382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48315583
X-RAY DIFFRACTIONr_chiral_restr0.0830.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023628
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02697
X-RAY DIFFRACTIONr_nbd_refined0.2490.3759
X-RAY DIFFRACTIONr_nbd_other0.2520.33091
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5260
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2170.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7510.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3191.51925
X-RAY DIFFRACTIONr_mcangle_it0.61423108
X-RAY DIFFRACTIONr_scbond_it1.12631319
X-RAY DIFFRACTIONr_scangle_it1.9784.51301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.412 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 135
Rwork0.36 1280
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)
12.0406-0.2830.6331.62670.23993.04590.1070.033-0.1069-0.0178-0.090.18520.0213-0.3833-0.01690.22930.049-0.00560.0435-0.01330.27739.6165.13914.553
24.3182.95770.11751.03910.81081.92410.27630.1025-0.06230.0142-0.17530.11630.2604-0.1397-0.1010.25860.0624-0.02280.0773-0.00720.218245.3831.69914.096
31.4569-1.553-0.83588.92642.9843.16670.18720.2815-0.1878-0.30050.0288-0.53350.19910.259-0.2160.39310.02270.00860.255-0.08060.530313.61230.80310.366
412.8844-2.8088-2.49912.5497-0.00075.3520.2084-0.30970.01180.2942-0.25570.8340.0537-0.72290.04740.49820.02190.0630.4537-0.17150.738217.34616.56927.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION2PC1 - 91 - 9
3X-RAY DIFFRACTION3AA181 - 277181 - 277
4X-RAY DIFFRACTION4BB1 - 992 - 100
Refinement
*PLUS
Lowest resolution: 19.8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.52
LS refinement shell
*PLUS
Lowest resolution: 2.41 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.359

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