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- PDB-6nf7: Crystal Structure of RT1.Aa-Bu31-10 -

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Basic information

Entry
Database: PDB / ID: 6nf7
TitleCrystal Structure of RT1.Aa-Bu31-10
Components
  • Beta-2-microglobulin
  • Bu31-10 peptide
  • RT1A.a
KeywordsIMMUNE SYSTEM / transplantation / tolerance / CD8+ Tregs / rat / MHC
Function / homology
Function and homology information


Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Downstream TCR signaling / Phosphorylation of CD3 and TCR zeta chains / Endosomal/Vacuolar pathway / DAP12 interactions / cellular response to morphine / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Generation of second messenger molecules ...Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Downstream TCR signaling / Phosphorylation of CD3 and TCR zeta chains / Endosomal/Vacuolar pathway / DAP12 interactions / cellular response to morphine / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Generation of second messenger molecules / ER-Phagosome pathway / positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / DAP12 signaling / MHC class II antigen presentation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / protein antigen binding / B cell affinity maturation / cellular response to glucocorticoid stimulus / Neutrophil degranulation / antigen processing and presentation / humoral immune response / toxic substance binding / defense response to fungus / response to cadmium ion / negative regulation of T cell proliferation / multivesicular body / cellular response to dexamethasone stimulus / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / cellular response to type II interferon / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / early endosome / learning or memory / immune response / response to xenobiotic stimulus / external side of plasma membrane / lysosomal membrane / signaling receptor binding / ubiquitin protein ligase binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha/beta chain, N-terminal / 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 ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha/beta chain, N-terminal / 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 / RT1 class I histocompatibility antigen, AA alpha chain / Rano class II histocompatibility antigen, B-1 beta chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsGras, S.
CitationJournal: Cell Rep / Year: 2019
Title: Cross-Reactive Donor-Specific CD8+Tregs Efficiently Prevent Transplant Rejection.
Authors: Picarda, E. / Bezie, S. / Usero, L. / Ossart, J. / Besnard, M. / Halim, H. / Echasserieau, K. / Usal, C. / Rossjohn, J. / Bernardeau, K. / Gras, S. / Guillonneau, C.
History
DepositionDec 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 11, 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 1.3Oct 23, 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: RT1A.a
B: Beta-2-microglobulin
C: Bu31-10 peptide
D: RT1A.a
E: Beta-2-microglobulin
F: Bu31-10 peptide
G: RT1A.a
H: Beta-2-microglobulin
I: Bu31-10 peptide
J: RT1A.a
K: Beta-2-microglobulin
L: Bu31-10 peptide
M: RT1A.a
N: Beta-2-microglobulin
O: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)226,83315
Polymers226,83315
Non-polymers00
Water00
1
A: RT1A.a
B: Beta-2-microglobulin
C: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)45,3673
Polymers45,3673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-18 kcal/mol
Surface area19130 Å2
MethodPISA
2
D: RT1A.a
E: Beta-2-microglobulin
F: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)45,3673
Polymers45,3673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-17 kcal/mol
Surface area19240 Å2
MethodPISA
3
G: RT1A.a
H: Beta-2-microglobulin
I: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)45,3673
Polymers45,3673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-15 kcal/mol
Surface area19460 Å2
MethodPISA
4
J: RT1A.a
K: Beta-2-microglobulin
L: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)45,3673
Polymers45,3673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-13 kcal/mol
Surface area19290 Å2
MethodPISA
5
M: RT1A.a
N: Beta-2-microglobulin
O: Bu31-10 peptide


Theoretical massNumber of molelcules
Total (without water)45,3673
Polymers45,3673
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-14 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.046, 205.860, 100.673
Angle α, β, γ (deg.)90.000, 103.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RT1A.a


Mass: 32045.551 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16391*PLUS
#2: Protein
Beta-2-microglobulin


Mass: 11783.478 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07151
#3: Protein/peptide
Bu31-10 peptide


Mass: 1537.632 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P29826*PLUS
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: 2.85 Å3/Da / Density % sol: 56.81 % / Mosaicity: 0.21 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M Bis-Tris-Propane pH 6.6, 28% PEG 8000 and 0.2 M Mg2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→47.864 Å / Num. obs: 52956 / % possible obs: 94.5 % / Redundancy: 4.2 % / CC1/2: 0.885 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.136 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.9-2.993.30.78644990.418192.9
11.96-47.8644.30.0527470.995190.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ED3

1ed3


Resolution: 2.9→47.864 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.98
RfactorNum. reflection% reflection
Rfree0.2748 2663 5.05 %
Rwork0.2074 --
obs0.2109 52702 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.43 Å2 / Biso mean: 39.9089 Å2 / Biso min: 9.64 Å2
Refinement stepCycle: final / Resolution: 2.9→47.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15902 0 0 0 15902
Num. residues----1922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316349
X-RAY DIFFRACTIONf_angle_d0.75622184
X-RAY DIFFRACTIONf_chiral_restr0.032262
X-RAY DIFFRACTIONf_plane_restr0.0032913
X-RAY DIFFRACTIONf_dihedral_angle_d15.6996115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.95270.3681370.3032517265491
2.9527-3.00950.29431200.27212625274594
3.0095-3.07090.33741320.26742666279894
3.0709-3.13770.34031460.26262609275594
3.1377-3.21070.36491480.26382650279894
3.2107-3.2910.34491240.25982594271894
3.291-3.37990.3071440.23442687283195
3.3799-3.47930.3511330.22972655278895
3.4793-3.59160.28651550.21422681283695
3.5916-3.71990.26331360.20392638277495
3.7199-3.86880.29091230.20912698282195
3.8688-4.04480.28391530.20322645279895
4.0448-4.25790.24261570.18432667282495
4.2579-4.52450.22831520.16512624277695
4.5245-4.87350.22981390.15872651279094
4.8735-5.36340.21491260.16762639276593
5.3634-6.13810.27131360.19162596273293
6.1381-7.72810.27171520.20022602275493
7.7281-47.87090.20021500.17142595274591

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