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- PDB-7tuc: Crystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF -

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Basic information

Entry
Database: PDB / ID: 7tuc
TitleCrystal structure of HLA-B*44:05 (T73C) with 9mer EEFGRAFSF
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • MHC class II antigen peptide
KeywordsIMMUNE SYSTEM / tapasin / histocompatibility complex class I / MHC-I / HLA / peptide editing / peptide loading complex / PLC / antigen presentation / immune response
Function / homology
Function and homology information


antigen processing and presentation / : / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / : / : / 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 / cellular response to iron ion / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal 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 II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / 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
Beta-2-microglobulin / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsJiang, J. / Natarajan, K. / Kim, E. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation.
Authors: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
P: MHC class II antigen peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1448
Polymers44,7743
Non-polymers3705
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-7 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 82.582, 110.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B alpha chain


Mass: 31804.158 Da / Num. of mol.: 1 / Mutation: T73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B44:05 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MHC class II antigen peptide


Mass: 1090.165 Da / Num. of mol.: 1 / Fragment: EEFGRAFSF
Source method: isolated from a genetically manipulated source
Details: HLA-DPA1*02:01 derived peptide 9mer / Source: (gene. exp.) Synthetic construct (others) / Gene: HLA-DPA1 / Production host: Synthetic construct (others) / References: UniProt: Q9TQB0

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Non-polymers , 3 types, 459 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 16% PEG 3350, 0.1M Tris, 0.2M Ca Acetate / PH range: 6.0-8.5

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Data collection

DiffractionMean temperature: 273 K / Ambient temp details: LN blow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→46.03 Å / Num. obs: 128295 / % possible obs: 95.43 % / Redundancy: 2 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0329 / Rpim(I) all: 0.0329 / Rrim(I) all: 0.0465 / Net I/σ(I): 11.61
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4125 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11969 / CC1/2: 0.555 / CC star: 0.845 / Rpim(I) all: 0.4125 / Rrim(I) all: 0.5834 / % possible all: 80.29

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6O

1m6o


Resolution: 1.25→46.03 Å / SU ML: 0.1071 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.0858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1936 1.57 %
Rwork0.1796 121482 -
obs0.1799 123418 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.53 Å2
Refinement stepCycle: LAST / Resolution: 1.25→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 24 454 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423283
X-RAY DIFFRACTIONf_angle_d0.80624456
X-RAY DIFFRACTIONf_chiral_restr0.0826454
X-RAY DIFFRACTIONf_plane_restr0.0077588
X-RAY DIFFRACTIONf_dihedral_angle_d13.08641232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.26061140.27346977X-RAY DIFFRACTION77.58
1.28-1.320.26521280.23928013X-RAY DIFFRACTION89.09
1.32-1.350.2471320.23288271X-RAY DIFFRACTION91.77
1.35-1.40.26081320.22938314X-RAY DIFFRACTION92.6
1.4-1.450.20181370.198610X-RAY DIFFRACTION95.19
1.45-1.510.19711400.17558682X-RAY DIFFRACTION96.33
1.51-1.570.18571410.16648795X-RAY DIFFRACTION97.73
1.57-1.660.18291410.16268921X-RAY DIFFRACTION98.61
1.66-1.760.20011440.17449020X-RAY DIFFRACTION99.26
1.76-1.90.21181440.17299026X-RAY DIFFRACTION99.45
1.9-2.090.18641430.16719077X-RAY DIFFRACTION99.57
2.09-2.390.18941440.17149134X-RAY DIFFRACTION99.73
2.39-3.010.19091460.18729208X-RAY DIFFRACTION99.79
3.01-46.030.17151500.16519434X-RAY DIFFRACTION98.8
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)
11.42654366084-0.522739648750.2039509526851.256032973860.02659041333030.6676822104450.06078712606040.0940459195657-0.110481310214-0.0714893095367-0.04852536126770.1159693990380.0411678092489-0.0783280363657-0.008218526186380.0585302296297-0.00500325960964-0.01316776461320.0505826491858-0.01290021230240.0615012283654-10.20956882075.7543262714-30.7662412001
21.41958780584-0.04577488241660.2233279596190.5741765226740.05143716668260.39673559732-0.007930339853450.1298323734490.111174961526-0.0580698804951-0.0111044426979-0.032495474312-0.02687110874110.01547868592870.01227490753590.0637330292850.00300771307882-0.00161962311820.05086246483080.01020445184720.0517133759394-0.30754361061116.3093042207-31.0281544107
30.4530251730720.0726139304822-0.4694655073350.6125550042740.0700085501292.807849489460.0211982720278-0.10715652756-0.01376172737290.1366856823680.02993949389380.0321116946727-0.148877672791-0.0353841072218-0.02658962238050.08353597952430.01268148128460.007360984590510.09894173595620.0002544498237540.0715666770613-25.232455191415.7189073303-3.8331306691
47.890947621451.903230714020.5673297718722.34398455905-0.0743096062942.037137449430.0137361044969-0.186097828715-0.2313257826780.0372110552007-0.073222774639-0.0918963868127-0.07786070561220.1850071819620.06117454168290.0892858968230.005631185446970.007184772811480.0872340739550.02634454821180.0625443735065-9.732920841683.52678597193-8.98693952742
55.124561766652.89068262428-1.482873660061.6743848964-0.6613710681351.12722789233-0.06503644064240.124500180133-0.03921358068740.1160477115340.1422780980990.5952454929050.257828016944-0.640547371926-0.1066371425820.130078776192-0.03702836385360.04879062739240.2022853148140.04474154804570.290079469175-32.1758109534-1.74964652977-10.0167109748
66.08207430493.40860336077-1.550463185933.54317413979-0.7251023971322.11841934737-0.05733404516230.012829884108-0.0368032533206-0.09533183252350.006986825633920.2643661616780.108366593959-0.1509502111550.05300119112220.0639547148010.00475548505226-0.004332131512160.04437723876530.006100833645560.083896916228-17.73535712230.34268354296-13.1180813751
76.970428578136.47747152896-3.211538300617.08880972886-2.563721974272.26910364835-0.4296860336870.0545887764441-0.453518285333-0.3608872330460.179916537032-0.2275968204970.302148524006-0.009069420149190.2221846522980.134320362030.01498601194320.04167313911770.08536385753120.02633665948520.140200446232-8.56776694742-4.84936801611-13.6452127648
82.693952815410.7019711771690.16333940783.256535385011.050880055380.340684318192-0.1557280615130.0257629122101-0.481912097934-0.2360637735220.04566901827210.1729884735230.4056670785590.07541711231070.07309694918160.262006687731-0.001367192130620.05291389779350.0999429795853-0.0124102128330.226608800246-17.2670658262-11.8902541169-15.0836149918
97.683490839064.524318304040.8407597155365.673650652891.87748364870.72709383767-0.05272891654830.427042452164-0.248159710986-0.3332064131940.1559898783490.1809105598720.506346314457-0.0493928534569-0.1048621023390.181924768729-0.00598832098619-0.04183184180280.0902270703811-0.006751824323670.0758125934391-9.671651818245.29088872076-22.4499045128
104.176370674882.37791651058-1.361492364782.9023138966-1.0656914221.69997551091-0.00420479945888-0.03372011267140.0436528956304-0.103396712266-0.01285313999580.250276498250.0480023875608-0.05954088642910.01960655283270.07512131676020.007624017484080.005544140132680.0468017693641-0.01173915994090.0789624641439-13.65685012212.96433341829-16.6098892792
110.7273838866410.799491375787-0.2780817461661.2061832584-0.8101167647390.8838132891790.0316469084252-0.605094445666-0.4129999399550.3083263127950.008665364243960.36644807540.300753055885-0.349841586462-0.03774738323480.35948350705-0.06994065623940.1267185853030.3276234953950.08970095598340.37846766824-28.0273800395-11.0979441482-2.58218217464
120.353893201517-0.46213319257-0.3062794906180.6880323250940.1117697219011.249234394030.018594868259-0.282305704073-0.3986102004150.230096035443-0.148940930067-0.2049784808240.1488513784240.197404603520.05391040520020.1483402545450.03114902997480.01194652808080.1557155998360.1128533699030.206888190914-7.20319428997-5.76593606168-7.32160776284
135.60422642685-1.33127226096-0.04547998245533.39321712114-0.2101681536663.53961745151-0.145454557745-0.624808989727-0.3434111460720.455484594365-0.03787745297960.1907953524470.05153676204350.01247689604980.1571935087080.212158024899-0.009581466087670.05898308563660.1942608614150.04495175175450.142158560125-19.8818054919-2.07289919048-2.32660538518
147.200930829670.4502138863172.481506430421.060453077240.04011307029341.51339072461-0.03887118874050.6164035290570.296284058076-0.0898971076033-0.0198353854287-0.1255687921360.02898856768870.162649656230.08192165351260.1376335430430.0127326219070.009284380891030.1414226608270.01315425788730.117895250226-0.086174013448515.1243549409-37.1733229695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 56 )AA1 - 561 - 56
22chain 'A' and (resid 57 through 174 )AA57 - 17457 - 174
33chain 'A' and (resid 175 through 274 )AA175 - 274175 - 274
44chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
55chain 'B' and (resid 12 through 19 )BB12 - 1912 - 19
66chain 'B' and (resid 20 through 30 )BB20 - 3020 - 30
77chain 'B' and (resid 31 through 41 )BB31 - 4131 - 41
88chain 'B' and (resid 42 through 51 )BB42 - 5142 - 51
99chain 'B' and (resid 52 through 56 )BB52 - 5652 - 56
1010chain 'B' and (resid 57 through 71 )BB57 - 7157 - 71
1111chain 'B' and (resid 72 through 77 )BB72 - 7772 - 77
1212chain 'B' and (resid 78 through 90 )BB78 - 9078 - 90
1313chain 'B' and (resid 91 through 99 )BB91 - 9991 - 99
1414chain 'P' and (resid 1 through 9 )PC1 - 91 - 9

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