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- PDB-6a2b: Crystal Structure of Xenopus laevis MHC I complex -

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Basic information

Entry
Database: PDB / ID: 6a2b
TitleCrystal Structure of Xenopus laevis MHC I complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • TYR-MET-MET-PRO-ARG-HIS-TRP-PRO-ILE
KeywordsIMMUNE SYSTEM / Xenopus laevis / MHC I / evolution
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / extracellular region / membrane
Similarity search - Function
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 / : ...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 / MHC class I antigen
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMa, L.Z. / Xia, C.
CitationJournal: J Immunol. / Year: 2020
Title: A Glimpse of the Peptide Profile Presentation byXenopus laevisMHC Class I: Crystal Structure of pXela-UAA Reveals a Distinct Peptide-Binding Groove.
Authors: Ma, L. / Zhang, N. / Qu, Z. / Liang, R. / Zhang, L. / Zhang, B. / Meng, G. / Dijkstra, J.M. / Li, S. / Xia, M.C.
History
DepositionJun 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: TYR-MET-MET-PRO-ARG-HIS-TRP-PRO-ILE


Theoretical massNumber of molelcules
Total (without water)43,8203
Polymers43,8203
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-30 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.139, 68.220, 107.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31644.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TPA7
#2: Protein Beta-2-microglobulin


Mass: 10942.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: b2m / Production host: Escherichia coli (E. coli) / References: UniProt: Q9IA97
#3: Protein/peptide TYR-MET-MET-PRO-ARG-HIS-TRP-PRO-ILE


Mass: 1232.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli)

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium malonate pH6.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.987 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 29548 / % possible obs: 92.5 % / Redundancy: 2 % / CC1/2: 0.939 / Rmerge(I) obs: 0.188 / Net I/σ(I): 2.6
Reflection shellResolution: 2.8→2.83 Å / Num. unique obs: 4256 / CC1/2: 0.926 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R

4e0r


Resolution: 2.8→14.98 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.836 / SU B: 17.21 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26437 445 5 %RANDOM
Rwork0.20004 ---
obs0.22595 8405 78.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.8→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 0 3086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193175
X-RAY DIFFRACTIONr_bond_other_d0.0020.022772
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.934307
X-RAY DIFFRACTIONr_angle_other_deg1.08736461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9545372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34423.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.78315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2981523
X-RAY DIFFRACTIONr_chiral_restr0.1050.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02670
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 2 -
Rwork0.301 25 -
obs--3.49 %

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