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- PDB-7nmd: Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL -

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Basic information

Entry
Database: PDB / ID: 7nmd
TitleHuman Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL
Components
  • GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
  • Human MHC Class I, beta 2 microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC Class I / A24 / Diabetes related super antigen
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Cole, D.K.
CitationJournal: To Be Published
Title: Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL
Authors: Rizkallahp, P.J. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Human MHC Class I, beta 2 microglobulin
C: GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
D: MHC class I antigen
E: Human MHC Class I, beta 2 microglobulin
F: GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,21926
Polymers89,5106
Non-polymers1,71020
Water4,306239
1
A: MHC class I antigen
B: Human MHC Class I, beta 2 microglobulin
C: GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,81215
Polymers44,7553
Non-polymers1,05712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-54 kcal/mol
Surface area18860 Å2
MethodPISA
2
D: MHC class I antigen
E: Human MHC Class I, beta 2 microglobulin
F: GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,40711
Polymers44,7553
Non-polymers6538
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-29 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.543, 48.662, 123.141
Angle α, β, γ (deg.)90.000, 105.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31778.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411J078
#2: Protein Human MHC Class I, beta 2 microglobulin / Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU


Mass: 1097.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 259 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1 M TRIS (pH 7.5), 15% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→74.01 Å / Num. obs: 43149 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.984 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.089 / Rrim(I) all: 0.174 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.313.61.2171140631790.40.7411.43198.3
10.06-73.993.40.05718435430.9680.0380.06913.699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.92 Å74.01 Å
Translation3.92 Å74.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.3data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.25→74.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 21.485 / SU ML: 0.244 / SU R Cruickshank DPI: 0.3268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 2050 4.8 %RANDOM
Rwork0.2094 ---
obs0.2121 41059 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.07 Å2 / Biso mean: 47.57 Å2 / Biso min: 24.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.84 Å2
2---1.29 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.25→74.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 104 239 6649
Biso mean--74.43 46.1 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136577
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175915
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.668890
X-RAY DIFFRACTIONr_angle_other_deg1.1941.58413638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0385766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24721.429406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.191151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2311558
X-RAY DIFFRACTIONr_chiral_restr0.0660.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021602
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.372 141 -
Rwork0.316 2978 -
obs--96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1784-1.42850.23280.9980.20362.71650.03250.3058-0.13060.0378-0.04290.01510.0925-0.40730.01040.0552-0.0098-0.12140.16620.00510.294923.6224-12.593713.1229
22.0831-0.1976-2.03362.51622.10288.6625-0.1505-0.3720.01940.6225-0.00760.34420.5227-0.31690.15810.23710.0222-0.07990.19320.00610.403127.8954-13.270849.1702
33.1627-0.12662.03792.6571-0.3685.7674-0.0709-0.13080.23570.17570.0795-0.3093-0.51440.3321-0.00860.1268-0.0475-0.14520.0707-0.01210.347337.8732-0.507133.4322
43.2477-1.04970.34371.1338-0.23672.17290.1448-0.0591-0.15680.0733-0.09480.077-0.04140.3348-0.050.0792-0.0346-0.1180.2952-0.04510.270862.280510.457212.3327
52.49010.5759-0.49752.90581.04098.4191-0.1155-0.31680.0910.55870.02030.20350.37920.03960.09520.2257-0.0551-0.13640.55110.01890.366667.1616.749448.3372
62.7303-0.30222.44142.0641-0.62736.4613-0.0675-0.1670.40070.4289-0.1725-0.4105-0.79570.95970.240.2906-0.3226-0.18530.7171-0.03650.388977.247220.392433.2753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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