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- PDB-7zqj: MHC class I from a wild bird in complex with a nonameric peptide P3 -

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Basic information

Entry
Database: PDB / ID: 7zqj
TitleMHC class I from a wild bird in complex with a nonameric peptide P3
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Uncharacterized protein Rv3403c
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex Class I / Acrocephalus arundinaceus / antigen presentation / cell-surface receptor / nonameric peptide from Mycobacterium
Function / homology
Function and homology information


response to metal ion / 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 / plasma membrane
Similarity search - Function
FAD-dependent urate hydroxylase HpyO, FAD/NAD(P)-binding domain / : / FAD-NAD(P)-binding / 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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...FAD-dependent urate hydroxylase HpyO, FAD/NAD(P)-binding domain / : / FAD-NAD(P)-binding / 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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / FAD/NAD(P)-binding domain superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-2-microglobulin / MHC class I antigen / Uncharacterized protein Rv3403c
Similarity search - Component
Biological speciesAcrocephalus arundinaceus (great reed warbler)
Mycobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsEltschkner, S. / Mellinger, S. / Buus, S. / Nielsen, M. / Paulsson, K.M. / Lindkvist-Petersson, K. / Westerdahl, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)679799European Union
CitationJournal: Front Immunol / Year: 2023
Title: The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus.
Authors: Eltschkner, S. / Mellinger, S. / Buus, S. / Nielsen, M. / Paulsson, K.M. / Lindkvist-Petersson, K. / Westerdahl, H.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
F: Uncharacterized protein Rv3403c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0295
Polymers46,8743
Non-polymers1552
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-45 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.793, 65.977, 122.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31630.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: exon 2-4
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Organ: liver / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O98187
#2: Protein Beta-2-microglobulin


Mass: 14205.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag, TEV-cleavage site
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076JEK1

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Protein/peptide , 1 types, 1 molecules F

#3: Protein/peptide Uncharacterized protein Rv3403c


Mass: 1038.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mycobacterium sp. (bacteria) / References: UniProt: P9WKZ5

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Non-polymers , 3 types, 78 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 6 % (v/v) Tacsimate, pH 6.0, 25 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.94 Å / Num. obs: 20176 / % possible obs: 99.5 % / Redundancy: 5.9 % / CC1/2: 0.995 / Net I/σ(I): 8.1
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1819 / CC1/2: 0.418 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJX

5gjx


Resolution: 2.25→46.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.01 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23099 982 4.9 %RANDOM
Rwork0.19754 ---
obs0.19919 19145 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: 1 / Resolution: 2.25→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 9 76 3177
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 70 -
Rwork0.302 1378 -
obs--99.66 %

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