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- PDB-8hso: CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q... -

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Basic information

Entry
Database: PDB / ID: 8hso
TitleCRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Components
  • Beta-2-microglobulin
  • Ig-like domain-containing protein
  • PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
KeywordsIMMUNE SYSTEM / MHC / IMMUNOLIGY / IMMUNE SYSTEM TRANSFERASE COMPLEX.
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / immune response / signaling receptor binding ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / immune response / signaling receptor binding / external side of plasma membrane / extracellular space / extracellular region
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig-like domain-containing protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesMyotis lucifugus (little brown bat)
Pteropus alecto (black flying fox)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, S.Q. / Zhang, N.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2024
Title: Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Authors: Wang, S. / Zheng, L. / Wei, X. / Qu, Z. / Du, L. / Wang, S. / Zhang, N.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Jan 1, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig-like domain-containing protein
B: Beta-2-microglobulin
C: PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)43,8573
Polymers43,8573
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-17 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.265, 81.832, 144.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ig-like domain-containing protein


Mass: 31441.793 Da / Num. of mol.: 1 / Mutation: 52M,53Q,54Q,55P,56W DELETED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myotis lucifugus (little brown bat) / Gene: B-67 / Production host: Escherichia coli (E. coli) / References: UniProt: G1PNR4
#2: Protein Beta-2-microglobulin


Mass: 11474.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10023531 / Production host: Escherichia coli (E. coli) / References: UniProt: L5K3Y9
#3: Protein/peptide PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL


Mass: 940.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.0 M Ammonium sulfate 0.1 M Sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19652 / % possible obs: 97.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.071
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1419 / Rpim(I) all: 0.084

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.902 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27222 914 5.3 %RANDOM
Rwork0.22777 ---
obs0.23014 16306 64.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 0 53 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172768
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6574343
X-RAY DIFFRACTIONr_angle_other_deg1.1861.586441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1935379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90121.795195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6391525
X-RAY DIFFRACTIONr_chiral_restr0.0670.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
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_it2.7834.1651525
X-RAY DIFFRACTIONr_mcbond_other2.7814.1651524
X-RAY DIFFRACTIONr_mcangle_it4.3366.2431901
X-RAY DIFFRACTIONr_mcangle_other4.3366.2431902
X-RAY DIFFRACTIONr_scbond_it2.7284.4291667
X-RAY DIFFRACTIONr_scbond_other2.7274.4291668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3816.5342443
X-RAY DIFFRACTIONr_long_range_B_refined6.69347.0793435
X-RAY DIFFRACTIONr_long_range_B_other6.69347.0823435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å /
RfactorNum. reflection
Rfree0.284 5
Rwork-171

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