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- PDB-5f1i: MHC with 9-mer peptide -

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Basic information

Entry
Database: PDB / ID: 5f1i
TitleMHC with 9-mer peptide
Components
  • 9-mer peptide
  • Beta2M
  • MHC class I DLA-88
KeywordsIMMUNE SYSTEM / MHC
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / 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-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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsLiu, J. / Chai, Y. / QI, J. / Gao, G.F.
CitationJournal: J Immunol. / Year: 2016
Title: Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I
Authors: Xiao, J. / Xiang, W. / Chai, Y. / Haywood, J. / Qi, J. / Ba, L. / Qi, P. / Wang, M. / Liu, J. / Gao, G.F.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 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 DLA-88
B: Beta2M
C: 9-mer peptide
D: MHC class I DLA-88
E: Beta2M
F: 9-mer peptide
G: MHC class I DLA-88
H: Beta2M
I: 9-mer peptide
J: MHC class I DLA-88
K: Beta2M
L: 9-mer peptide
M: MHC class I DLA-88
N: Beta2M
O: 9-mer peptide
P: MHC class I DLA-88
Q: Beta2M
R: 9-mer peptide
S: MHC class I DLA-88
T: Beta2M
U: 9-mer peptide
V: MHC class I DLA-88
W: Beta2M
X: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)354,68124
Polymers354,68124
Non-polymers00
Water00
1
A: MHC class I DLA-88
B: Beta2M
C: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-17 kcal/mol
Surface area18890 Å2
MethodPISA
2
D: MHC class I DLA-88
E: Beta2M
F: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-16 kcal/mol
Surface area19000 Å2
MethodPISA
3
G: MHC class I DLA-88
H: Beta2M
I: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-19 kcal/mol
Surface area19230 Å2
MethodPISA
4
J: MHC class I DLA-88
K: Beta2M
L: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area19140 Å2
MethodPISA
5
M: MHC class I DLA-88
N: Beta2M
O: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-18 kcal/mol
Surface area18970 Å2
MethodPISA
6
P: MHC class I DLA-88
Q: Beta2M
R: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17 kcal/mol
Surface area19540 Å2
MethodPISA
7
S: MHC class I DLA-88
T: Beta2M
U: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-19 kcal/mol
Surface area19490 Å2
MethodPISA
8
V: MHC class I DLA-88
W: Beta2M
X: 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-15 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.101, 94.626, 124.355
Angle α, β, γ (deg.)84.60, 72.79, 81.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MHC class I DLA-88 / DLA-88*50801


Mass: 31562.742 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: J9UGS3
#2: Protein
Beta2M


Mass: 11748.160 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: P61769*PLUS
#3: Protein/peptide
9-mer peptide


Mass: 1024.211 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Canis lupus familiaris (dog)
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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M potassium thiocyanate, pH 7.0, 20% PEG 3350 (w/v), 30% 1,4-Dioxane (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.696→50 Å / Num. obs: 97116 / % possible obs: 97.9 % / Redundancy: 2.3 % / Net I/σ(I): 6.322

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPG

2xpg


Resolution: 2.904→41.545 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 3816 4.98 %
Rwork0.2085 --
obs0.2101 76658 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.904→41.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24650 0 0 0 24650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925335
X-RAY DIFFRACTIONf_angle_d1.4834436
X-RAY DIFFRACTIONf_dihedral_angle_d26.4269348
X-RAY DIFFRACTIONf_chiral_restr0.093582
X-RAY DIFFRACTIONf_plane_restr0.0054508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9039-2.94070.3164900.25631867X-RAY DIFFRACTION67
2.9407-2.97940.30561260.23742418X-RAY DIFFRACTION85
2.9794-3.02020.30291230.25322587X-RAY DIFFRACTION92
3.0202-3.06330.29761400.25242680X-RAY DIFFRACTION96
3.0633-3.1090.34041470.26622770X-RAY DIFFRACTION98
3.109-3.15760.3321320.25172746X-RAY DIFFRACTION98
3.1576-3.20930.26691580.2382728X-RAY DIFFRACTION98
3.2093-3.26460.28551430.22612789X-RAY DIFFRACTION98
3.2646-3.3240.28471620.22632692X-RAY DIFFRACTION98
3.324-3.38790.26491440.22862802X-RAY DIFFRACTION98
3.3879-3.4570.30961520.22922715X-RAY DIFFRACTION98
3.457-3.53210.28151480.22572768X-RAY DIFFRACTION98
3.5321-3.61430.24941360.21682757X-RAY DIFFRACTION98
3.6143-3.70460.25051580.22272731X-RAY DIFFRACTION98
3.7046-3.80470.27011560.21862779X-RAY DIFFRACTION98
3.8047-3.91660.23871140.21162743X-RAY DIFFRACTION98
3.9166-4.04290.20651300.21052787X-RAY DIFFRACTION98
4.0429-4.18720.24261340.19352780X-RAY DIFFRACTION98
4.1872-4.35470.24361200.1892755X-RAY DIFFRACTION98
4.3547-4.55270.21921530.18512780X-RAY DIFFRACTION98
4.5527-4.79240.19981590.17252731X-RAY DIFFRACTION98
4.7924-5.09210.19431440.18512732X-RAY DIFFRACTION98
5.0921-5.48450.2111650.19552760X-RAY DIFFRACTION98
5.4845-6.03490.21451630.19872725X-RAY DIFFRACTION98
6.0349-6.90480.23171490.21172721X-RAY DIFFRACTION97
6.9048-8.68620.21481270.1892807X-RAY DIFFRACTION100
8.6862-41.54970.17841430.19272692X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 29.2786 Å / Origin y: -11.769 Å / Origin z: -31.0463 Å
111213212223313233
T0.3972 Å20.0061 Å2-0.0075 Å2-0.3839 Å2-0.0031 Å2--0.398 Å2
L0.0713 °20.0154 °2-0.0255 °2-0.0788 °20.0031 °2--0.0633 °2
S-0.0149 Å °0.0045 Å °-0.0162 Å °0.0056 Å °-0.0073 Å °-0.0038 Å °-0.0125 Å °-0.0011 Å °0.0157 Å °
Refinement TLS groupSelection details: all

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