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- PDB-9qg8: Crystal structure of the great reed warbler MHC class I in comple... -

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Basic information

Entry
Database: PDB / ID: 9qg8
TitleCrystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide
Components
  • Beta-2-microglobulin
  • LYS-THR-MET-MET-ALA-HIS-ASP-LEU
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC class I / great reed warbler / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / external side of plasma membrane / extracellular space / extracellular region / metal ion binding
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / 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 ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesAcrocephalus arundinaceus (great reed warbler)
Legionella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVenskutonyte, R. / Lindkvist-Petersson, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)679799European Union
CitationJournal: Immunology / Year: 2025
Title: MHC I of the Great Reed Warbler Promotes a Flat Peptide Binding Mode.
Authors: Venskutonyte, R. / Kjellstrom, S. / O'Connor, E.A. / Westerdahl, H. / Lindkvist-Petersson, K.
History
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
K: LYS-THR-MET-MET-ALA-HIS-ASP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3379
Polymers46,7843
Non-polymers5536
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-26 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.947, 49.038, 39.380
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31630.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Production host: Escherichia coli (E. coli) / References: UniProt: O98187
#2: Protein Beta-2-microglobulin


Mass: 14205.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: A0A076JEK1
#3: Protein/peptide LYS-THR-MET-MET-ALA-HIS-ASP-LEU


Mass: 948.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Legionella (bacteria)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28 % PEG4000, 0.1 M MgCl2 and 0.1 M Tris/HCl pH 8.5 with seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.15→47.7 Å / Num. obs: 21449 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Χ2: 0.94 / Net I/σ(I): 10.7 / Num. measured all: 72011
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.733 / Num. measured all: 6284 / Num. unique obs: 1838 / CC1/2: 0.753 / Rpim(I) all: 0.468 / Rrim(I) all: 0.872 / Χ2: 0.95 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.7 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1116 5.21 %
Rwork0.2057 --
obs0.2089 21416 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 36 85 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033225
X-RAY DIFFRACTIONf_angle_d0.5454365
X-RAY DIFFRACTIONf_dihedral_angle_d20.1411198
X-RAY DIFFRACTIONf_chiral_restr0.044432
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.32171430.26732513X-RAY DIFFRACTION100
2.25-2.370.30281280.26012517X-RAY DIFFRACTION99
2.37-2.510.30151450.25192524X-RAY DIFFRACTION100
2.51-2.710.3221370.24872527X-RAY DIFFRACTION100
2.71-2.980.31961290.24012550X-RAY DIFFRACTION99
2.98-3.410.26081390.21422525X-RAY DIFFRACTION99
3.41-4.30.25821550.18532517X-RAY DIFFRACTION99
4.3-47.70.2321400.17892627X-RAY DIFFRACTION99

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