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- PDB-8ht1: CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q... -

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Basic information

Entry
Database: PDB / ID: 8ht1
TitleCRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Components
  • Beta-2-microglobulin
  • Ig-like domain-containing protein
  • THR-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: 2.4 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 1.1Oct 16, 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: THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL


Theoretical massNumber of molelcules
Total (without water)43,8113
Polymers43,8113
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-16 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.756, 81.034, 143.796
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 THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL


Mass: 893.962 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.: 71 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Calcium acetate hydrate 0.1 M Sodium cacodylate 12 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / 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: 1.98→50 Å / Num. obs: 17684 / % possible obs: 99.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 19.636
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 1.271 / Num. unique obs: 1403

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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: 2.4→43.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.775 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27684 840 4.8 %RANDOM
Rwork0.20819 ---
obs0.21125 16764 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.743 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å2-0 Å2
2--3.75 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.4→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 0 71 3161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133187
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172765
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6584337
X-RAY DIFFRACTIONr_angle_other_deg1.2611.586435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7845379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42921.804194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5791525
X-RAY DIFFRACTIONr_chiral_restr0.0740.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
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_it3.6084.5731525
X-RAY DIFFRACTIONr_mcbond_other3.6074.5741524
X-RAY DIFFRACTIONr_mcangle_it5.2326.8461901
X-RAY DIFFRACTIONr_mcangle_other5.2316.8461902
X-RAY DIFFRACTIONr_scbond_it3.9854.9861662
X-RAY DIFFRACTIONr_scbond_other3.9844.9851663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0787.3062437
X-RAY DIFFRACTIONr_long_range_B_refined8.13151.6673405
X-RAY DIFFRACTIONr_long_range_B_other8.13351.6563402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 73 -
Rwork0.235 1209 -
obs--100 %

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