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- PDB-5f1n: MHC complexed to 11mer peptide -

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Basic information

Entry
Database: PDB / ID: 5f1n
TitleMHC complexed to 11mer peptide
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1
KeywordsIMMUNE SYSTEM / MHC
Function / homology
Function and homology information


Endogenous sterols / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / trabecular meshwork development / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / retinal blood vessel morphogenesis / toxin metabolic process / blood vessel endothelial cell migration ...Endogenous sterols / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / trabecular meshwork development / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / retinal blood vessel morphogenesis / toxin metabolic process / blood vessel endothelial cell migration / arachidonate metabolic process / retinal metabolic process / estrogen 16-alpha-hydroxylase activity / negative regulation of cell adhesion mediated by integrin / collagen fibril organization / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / retinol metabolic process / estrogen metabolic process / regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to oxidative stress / antigen processing and presentation of peptide antigen via MHC class I / : / positive regulation of vascular endothelial growth factor production / nitric oxide biosynthetic process / xenobiotic metabolic process / negative regulation of cell migration / lumenal side of endoplasmic reticulum membrane / positive regulation of receptor signaling pathway via JAK-STAT / MHC class I protein complex / cellular response to hydrogen peroxide / response to toxic substance / phagocytic vesicle membrane / positive regulation of angiogenesis / angiogenesis / immune response / positive regulation of apoptotic process / iron ion binding / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / mitochondrion / extracellular region
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Cytochrome P450, E-class, group I / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / 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 / : / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
Cytochrome P450 family 1 subfamily B member 1 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1
D: MHC class I antigen
E: Beta-2-microglobulin
F: Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1


Theoretical massNumber of molelcules
Total (without water)94,4016
Polymers94,4016
Non-polymers00
Water10,503583
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1


Theoretical massNumber of molelcules
Total (without water)47,2013
Polymers47,2013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-20 kcal/mol
Surface area18370 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1


Theoretical massNumber of molelcules
Total (without water)47,2013
Polymers47,2013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-22 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.312, 160.492, 64.481
Angle α, β, γ (deg.)90.00, 104.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31562.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: DLA-88 / Production host: Escherichia coli (E. coli) / References: UniProt: J9UGS3
#2: Protein Beta-2-microglobulin


Mass: 14281.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: E2RN10
#3: Protein/peptide Peptide from Cytochrome P450 family 1 subfamily B polypeptide 1


Mass: 1356.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Canis lupus familiaris (dog) / References: UniProt: C1KG39
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris (pH 5.5), 25% PEG 3,350 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 64847 / % possible obs: 99.4 % / Redundancy: 4.2 % / Net I/σ(I): 15.997

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CNSdata reduction
CNSdata scaling
PHASESphasing
RefinementResolution: 2→31.454 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 3278 5.06 %
Rwork0.1836 --
obs0.1855 64761 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→31.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 583 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076458
X-RAY DIFFRACTIONf_angle_d0.9968772
X-RAY DIFFRACTIONf_dihedral_angle_d15.3012372
X-RAY DIFFRACTIONf_chiral_restr0.045904
X-RAY DIFFRACTIONf_plane_restr0.0051162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9985-2.02830.27581280.22652302X-RAY DIFFRACTION85
2.0283-2.060.27661550.22832672X-RAY DIFFRACTION99
2.06-2.09380.28451280.22742659X-RAY DIFFRACTION99
2.0938-2.12990.26291500.21742673X-RAY DIFFRACTION99
2.1299-2.16860.25671290.21492703X-RAY DIFFRACTION99
2.1686-2.21030.25791670.21382681X-RAY DIFFRACTION100
2.2103-2.25540.27181360.21952674X-RAY DIFFRACTION99
2.2554-2.30440.2531340.21372707X-RAY DIFFRACTION99
2.3044-2.3580.25421440.20452665X-RAY DIFFRACTION99
2.358-2.4170.27651490.19572652X-RAY DIFFRACTION100
2.417-2.48230.24361510.20112714X-RAY DIFFRACTION100
2.4823-2.55530.25111270.19972685X-RAY DIFFRACTION100
2.5553-2.63770.24191380.20132696X-RAY DIFFRACTION100
2.6377-2.7320.23031390.20242745X-RAY DIFFRACTION100
2.732-2.84130.23291480.20752655X-RAY DIFFRACTION100
2.8413-2.97050.22261490.1932699X-RAY DIFFRACTION100
2.9705-3.1270.23311540.18532686X-RAY DIFFRACTION100
3.127-3.32270.24351560.17972656X-RAY DIFFRACTION99
3.3227-3.57890.20051470.18352713X-RAY DIFFRACTION99
3.5789-3.93850.21411300.16842671X-RAY DIFFRACTION99
3.9385-4.50690.15811450.14872745X-RAY DIFFRACTION100
4.5069-5.67280.17541290.14742694X-RAY DIFFRACTION99
5.6728-31.45780.18611450.15982736X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.34 Å / Origin y: -12.7605 Å / Origin z: 140.8398 Å
111213212223313233
T0.1196 Å2-0.0135 Å2-0.0038 Å2-0.1578 Å20.0073 Å2--0.1269 Å2
L0.1608 °2-0.0939 °2-0.0521 °2-0.6147 °20.1618 °2--0.1814 °2
S-0.0143 Å °0.033 Å °-0.0049 Å °-0.0196 Å °-0.0024 Å °-0.0048 Å °-0.0262 Å °-0.0316 Å °-0 Å °
Refinement TLS groupSelection details: all

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