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- PDB-8d5n: Crystal structure of Ld-HF10 -

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Basic information

Entry
Database: PDB / ID: 8d5n
TitleCrystal structure of Ld-HF10
Components
  • Beta-2-microglobulin
  • Dense granule protein 6, HF10 peptide
  • H-2 class I histocompatibility antigen, L-D alpha chain
KeywordsIMMUNE SYSTEM / MHCI / antigen / CD8 T cell
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / defense response / 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 / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / 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
PROPANOIC ACID / Beta-2-microglobulin / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, Y. / Dai, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2022
Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response.
Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S.
History
DepositionJun 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
C: H-2 class I histocompatibility antigen, L-D alpha chain
E: Dense granule protein 6, HF10 peptide
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: Dense granule protein 6, HF10 peptide
F: Beta-2-microglobulin
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,72512
Polymers91,8916
Non-polymers8356
Water7,224401
1
C: H-2 class I histocompatibility antigen, L-D alpha chain
E: Dense granule protein 6, HF10 peptide
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4977
Polymers45,9453
Non-polymers5524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-12 kcal/mol
Surface area18740 Å2
MethodPISA
2
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: Dense granule protein 6, HF10 peptide
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2295
Polymers45,9453
Non-polymers2832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-21 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.503, 139.816, 87.344
Angle α, β, γ (deg.)90.000, 130.824, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules CAFH

#1: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 32402.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01897
#3: Protein Beta-2-microglobulin


Mass: 11975.634 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887

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Protein/peptide / Sugars , 2 types, 4 molecules EB

#2: Protein/peptide Dense granule protein 6, HF10 peptide


Mass: 1567.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: GRA6, TG24 / Production host: Podospora comata (fungus)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 405 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→77 Å / Num. obs: 102152 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.23 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 17831

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LD9

1ld9


Resolution: 1.8→50.005 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.178 / SU B: 5.793 / SU ML: 0.084 / Average fsc free: 0.8911 / Average fsc work: 0.9049 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2186 5081 5.049 %
Rwork0.1777 95555 -
all0.18 --
obs-100636 98.798 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.458 Å2-0 Å20.343 Å2
2---0.981 Å2-0 Å2
3---0.339 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6240 0 54 401 6695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0136509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175681
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6648843
X-RAY DIFFRACTIONr_angle_other_deg1.5421.58113219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4722.016377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.391151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261545
X-RAY DIFFRACTIONr_chiral_restr0.0990.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.027328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021455
X-RAY DIFFRACTIONr_nbd_refined0.2170.21134
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.25198
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23034
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.23023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2345
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.222
X-RAY DIFFRACTIONr_nbd_other0.1860.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.28
X-RAY DIFFRACTIONr_mcbond_it3.0473.4293080
X-RAY DIFFRACTIONr_mcbond_other3.0463.4283079
X-RAY DIFFRACTIONr_mcangle_it4.2155.1143840
X-RAY DIFFRACTIONr_mcangle_other4.2155.1143841
X-RAY DIFFRACTIONr_scbond_it4.3753.9563429
X-RAY DIFFRACTIONr_scbond_other4.3753.9573430
X-RAY DIFFRACTIONr_scangle_it6.5645.7215002
X-RAY DIFFRACTIONr_scangle_other6.5645.7225003
X-RAY DIFFRACTIONr_lrange_it8.34539.5457219
X-RAY DIFFRACTIONr_lrange_other8.34539.557220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3593960.36666480.36675600.6650.65993.17460.366
1.847-1.8970.3313810.31468890.31572990.7940.80799.60270.314
1.897-1.9520.3194030.28966670.29170990.8260.84299.59150.289
1.952-2.0120.2983240.24665740.24969280.8750.88599.5670.246
2.012-2.0780.2882950.22863440.23166710.8840.89899.52030.228
2.078-2.1510.2493260.20261160.20565010.9130.92799.09240.202
2.151-2.2320.2223280.18558260.18762350.930.9498.70090.185
2.232-2.3230.2193090.17557100.17760380.9320.94699.68530.175
2.323-2.4260.2212790.17454870.17657790.9380.94499.7750.174
2.426-2.5440.2142920.16252080.16555190.9430.95599.65570.162
2.544-2.6810.2032390.16449700.16652430.9480.95699.35150.164
2.681-2.8430.2322600.16846310.17149750.9260.94998.31160.168
2.843-3.0390.2132180.16744570.16946840.9420.95599.80790.167
3.039-3.2810.2171920.16941410.17143580.9440.95499.42630.169
3.281-3.5930.2022070.16737790.16940260.9530.96199.00650.167
3.593-4.0150.1721840.14734090.14836560.9650.96898.27680.147
4.015-4.6310.1591370.1330090.13131970.9670.97698.40480.13
4.631-5.6590.1841340.14725670.14927260.9720.97799.08290.147
5.659-7.9530.2281110.20119780.20221230.9420.95298.39850.201
7.953-50.0050.263640.21311280.21612150.9360.95198.1070.213
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)
10.182-0.0630.02190.1449-0.07960.609-0.0409-0.02-0.0009-0.03240.04040.001-0.06040.02460.00040.0388-0.01650.00290.0203-0.01270.0362106.783767.610418.9321
22.22510.8655-1.65881.2326-1.7572.6213-0.0875-0.1427-0.06440.0649-0.0109-0.0832-0.06470.05180.09840.0177-0.00020.00860.0465-0.02910.0388112.531559.771737.3751
30.30670.13210.13810.35260.10320.0780.0274-0.012-0.0217-0.0256-0.0136-0.05290.0157-0.0275-0.01390.0355-0.0289-0.00220.04660.010.0092106.1027104.705218.2697
41.7979-1.1566-2.81370.89391.27866.29060.02070.125-0.0368-0.0493-0.05260.03130.0795-0.3030.03180.0253-0.0287-0.01380.05510.00870.013187.1096111.656612.6516
51.97850.0697-0.33280.42910.04890.0743-0.0211-0.01310.048-0.04720.0374-0.03020.0068-0.0164-0.01630.0154-0.0276-0.00180.06590.00180.011120.9383117.548720.7013
60.11690.049-0.22030.3595-0.0971.71790.01870.033-0.0307-0.04250.11460.0051-0.01560.002-0.13330.0295-0.0262-0.00660.0583-0.01630.0379102.157156.11754.4065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLC1 - 273
2X-RAY DIFFRACTION2ALLE1 - 15
3X-RAY DIFFRACTION3ALLA1 - 275
4X-RAY DIFFRACTION4ALLB1 - 12
5X-RAY DIFFRACTION5ALLF-2 - 99
6X-RAY DIFFRACTION6ALLH-3 - 99

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