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- PDB-6m2k: Uncommon structural features of rabbit MHC class I (RLA-A1) compl... -

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Basic information

Entry
Database: PDB / ID: 6m2k
TitleUncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-10
Components
  • Beta-2-microglobulin
  • RLA class I histocompatibility antigen, alpha chain 19-1
  • VP60-10
KeywordsIMMUNE SYSTEM / MHC I complex / VP60-10
Function / homology
Function and homology information


calicivirin / host cell endoplasmic reticulum / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / ribonucleoside triphosphate phosphatase activity ...calicivirin / host cell endoplasmic reticulum / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / ribonucleoside triphosphate phosphatase activity / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / RNA helicase activity / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / external side of plasma membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / 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 / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / MHC classes I/II-like antigen recognition protein / Picornavirus/Calicivirus coat protein / : / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RLA class I histocompatibility antigen, alpha chain 19-1 / Genome polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Rabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsZhang, Q.X. / Liu, K.F. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W.L. / Liu, P.P. / Zhao, Y.Z. / Gao, G.L. / Ding, C.M. ...Zhang, Q.X. / Liu, K.F. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W.L. / Liu, P.P. / Zhao, Y.Z. / Gao, G.L. / Ding, C.M. / Lyu, J.X. / Liu, W.J.
CitationJournal: J.Virol. / Year: 2020
Title: Strict Assembly Restriction of Peptides from Rabbit Hemorrhagic Disease Virus Presented by Rabbit Major Histocompatibility Complex Class I Molecule RLA-A1.
Authors: Zhang, Q. / Liu, K. / Yue, C. / Zhang, D. / Lu, D. / Xiao, W. / Liu, P. / Zhao, Y. / Gao, G. / Ding, C. / Lyu, J. / Liu, W.J.
History
DepositionFeb 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 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 1.3Nov 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
C: VP60-10
B: Beta-2-microglobulin
A: RLA class I histocompatibility antigen, alpha chain 19-1


Theoretical massNumber of molelcules
Total (without water)44,5903
Polymers44,5903
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-22 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.612, 74.303, 152.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide VP60-10


Mass: 1034.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rabbit hemorrhagic disease virus / References: UniProt: P27410*PLUS
#2: Protein Beta-2-microglobulin / Beta2m


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein RLA class I histocompatibility antigen, alpha chain 19-1 / RLA-A1


Mass: 31676.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) / References: UniProt: P06140
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS PH 6.5, 20% w/v PEG 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03923 Å
DetectorType: SDMS / Detector: CMOS / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 18060 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 37.86 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 2.78
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.758 / Num. unique obs: 18060

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEG

5deg


Resolution: 2.59→29.97 Å / SU ML: 0.406 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.1048
RfactorNum. reflection% reflection
Rfree0.2938 745 5.07 %
Rwork0.215 --
obs0.219 14681 81.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.34 Å2
Refinement stepCycle: LAST / Resolution: 2.59→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 0 50 3196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843240
X-RAY DIFFRACTIONf_angle_d1.01844404
X-RAY DIFFRACTIONf_chiral_restr0.0581444
X-RAY DIFFRACTIONf_plane_restr0.0064582
X-RAY DIFFRACTIONf_dihedral_angle_d5.45921902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.4014950.30671774X-RAY DIFFRACTION52.9
2.79-3.080.36181360.29022301X-RAY DIFFRACTION68.4
3.08-3.520.3231550.2592879X-RAY DIFFRACTION85.01
3.52-4.430.29161720.20623394X-RAY DIFFRACTION98.48
4.43-29.970.24371870.16693588X-RAY DIFFRACTION99.71

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