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- PDB-7cpo: Crystal Structure of Anolis carolinensis MHC I complex -

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Basic information

Entry
Database: PDB / ID: 7cpo
TitleCrystal Structure of Anolis carolinensis MHC I complex
Components
  • HIS-VAL-TYR-GLY-PRO-LEU-LYS-PRO-ILE
  • MHC CLASS I ANTIGEN
  • beta2-microglobulin
KeywordsIMMUNE SYSTEM / MHC / IMMUNOLOGY
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
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
Ig-like domain-containing protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesAnolis carolinensis (green anole)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, Y. / Qu, Z. / Ma, L. / Wei, X. / Zhang, N. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Immunol. / Year: 2021
Title: The Crystal Structure of the MHC Class I (MHC-I) Molecule in the Green Anole Lizard Demonstrates the Unique MHC-I System in Reptiles.
Authors: Wang, Y. / Qu, Z. / Ma, L. / Wei, X. / Zhang, N. / Zhang, B. / Xia, C.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS I ANTIGEN
B: beta2-microglobulin
C: HIS-VAL-TYR-GLY-PRO-LEU-LYS-PRO-ILE


Theoretical massNumber of molelcules
Total (without water)45,3423
Polymers45,3423
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-19 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.919, 93.690, 246.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

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Components

#1: Protein MHC CLASS I ANTIGEN


Mass: 32757.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole) / Production host: Escherichia coli (E. coli) / References: UniProt: G1KTN1*PLUS
#2: Protein beta2-microglobulin


Mass: 11559.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole) / Production host: Escherichia coli (E. coli) / References: UniProt: H9GBW4*PLUS
#3: Protein/peptide HIS-VAL-TYR-GLY-PRO-LEU-LYS-PRO-ILE


Mass: 1025.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Potassium chloride, 0.1M Magnesium acetate tetrahydrate, 0.05M Sodium cacodylate trihydrate (pH 6.5), 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→19.92 Å / Num. obs: 72758 / % possible obs: 76.96 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.044 / Rrim(I) all: 0.15 / Net I/σ(I): 7.7
Reflection shellResolution: 2.09→2.39 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 9478 / CC1/2: 0.981 / Rpim(I) all: 0.107 / Rrim(I) all: 0.396 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.17.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJX

5gjx


Resolution: 2.5→19.92 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.9689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 1556 4.92 %
Rwork0.1854 30056 -
obs0.1884 31612 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 0 106 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093231
X-RAY DIFFRACTIONf_angle_d1.11494384
X-RAY DIFFRACTIONf_chiral_restr0.056441
X-RAY DIFFRACTIONf_plane_restr0.0074564
X-RAY DIFFRACTIONf_dihedral_angle_d10.7802422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.31831330.22032739X-RAY DIFFRACTION100
2.58-2.670.30491300.21262714X-RAY DIFFRACTION100
2.67-2.780.31541690.21332728X-RAY DIFFRACTION99.97
2.78-2.910.26531380.2052769X-RAY DIFFRACTION100
2.91-3.060.31371430.20952657X-RAY DIFFRACTION100
3.06-3.250.26581520.20782745X-RAY DIFFRACTION100
3.25-3.50.27911600.19622728X-RAY DIFFRACTION100
3.5-3.850.2491320.17382742X-RAY DIFFRACTION100
3.85-4.40.23441200.16412752X-RAY DIFFRACTION100
4.4-5.520.1821300.14782742X-RAY DIFFRACTION99.97
5.52-19.920.1781490.18472740X-RAY DIFFRACTION99.86

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