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- PDB-7tud: Crystal structure of HLA-B*44:05 (T73C) with 6mer EEFGRC and dipe... -

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Basic information

Entry
Database: PDB / ID: 7tud
TitleCrystal structure of HLA-B*44:05 (T73C) with 6mer EEFGRC and dipeptide GL
Components
  • Beta-2-microglobulin
  • EEFGRC peptide
  • GL dipeptide
  • HLA class I histocompatibility antigen, B alpha chain
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


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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Modulation by Mtb of host immune system / 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 / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / 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
Beta-2-Microglobulin / : / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Oct 30, 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: EEFGRC peptide
Q: GL dipeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8297
Polymers44,6134
Non-polymers2163
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-11 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.165, 79.757, 107.207
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: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 2 types, 2 molecules PQ

#3: Protein/peptide EEFGRC peptide


Mass: 740.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated synthetic peptide: 6mer / Source: (gene. exp.) Synthetic construct (others) / Production host: Synthetic construct (others)
#4: Protein/peptide GL dipeptide


Mass: 188.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic dipeptide: GL / Source: (gene. exp.) Synthetic construct (others) / Production host: Synthetic construct (others)

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Non-polymers , 3 types, 586 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 1500, 0.1M SPG (Succinic acid, Sodium phosphate monobasic monohydrate and Glycine)
PH range: 6.5-9.0

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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 EIGER2 X 16M / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→39.88 Å / Num. obs: 74712 / % possible obs: 98.96 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.31 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0713 / Rpim(I) all: 0.0362 / Rrim(I) all: 0.0803 / Net I/σ(I): 11.6
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.9425 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 7199 / CC1/2: 0.553 / CC star: 0.844 / Rpim(I) all: 0.5093 / % possible all: 97.01

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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: 1.45→39.88 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.1211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213 3735 5 %
Rwork0.1911 70977 -
obs0.1923 74712 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.48 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 14 583 3719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873254
X-RAY DIFFRACTIONf_angle_d0.92664419
X-RAY DIFFRACTIONf_chiral_restr0.0711453
X-RAY DIFFRACTIONf_plane_restr0.0068584
X-RAY DIFFRACTIONf_dihedral_angle_d13.10611219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.32611310.30562494X-RAY DIFFRACTION95.49
1.47-1.490.33041340.28052544X-RAY DIFFRACTION96.5
1.49-1.510.28351350.27952571X-RAY DIFFRACTION98.98
1.51-1.530.28331370.25482601X-RAY DIFFRACTION98.45
1.53-1.550.2491350.25862558X-RAY DIFFRACTION98.28
1.55-1.580.32631370.27622613X-RAY DIFFRACTION98.99
1.58-1.60.3131350.28632560X-RAY DIFFRACTION98.14
1.6-1.630.32091380.27352626X-RAY DIFFRACTION99.46
1.63-1.660.27191380.27192623X-RAY DIFFRACTION99.39
1.66-1.690.27221370.26042593X-RAY DIFFRACTION98.52
1.69-1.730.3071360.24812596X-RAY DIFFRACTION99.35
1.73-1.760.2651390.22732628X-RAY DIFFRACTION98.75
1.76-1.80.20981370.22382618X-RAY DIFFRACTION99.35
1.8-1.850.25841380.22612606X-RAY DIFFRACTION99.46
1.85-1.90.2491380.2222639X-RAY DIFFRACTION99.36
1.9-1.960.25221390.22612624X-RAY DIFFRACTION99.46
1.96-2.020.24861380.2122628X-RAY DIFFRACTION99.57
2.02-2.090.22791390.1922642X-RAY DIFFRACTION99.36
2.09-2.170.22781380.19692631X-RAY DIFFRACTION99.57
2.17-2.270.21041390.19552642X-RAY DIFFRACTION99.25
2.27-2.390.21611400.19172652X-RAY DIFFRACTION99.32
2.39-2.540.19511400.18972660X-RAY DIFFRACTION98.9
2.54-2.740.20861410.18522678X-RAY DIFFRACTION99.72
2.74-3.020.16661410.17492670X-RAY DIFFRACTION99.61
3.02-3.450.19981410.16012694X-RAY DIFFRACTION99.33
3.45-4.350.16031430.14292720X-RAY DIFFRACTION99.55
4.35-39.880.1721510.15542866X-RAY DIFFRACTION99.21
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)
15.16830887393-3.725131489880.7080852717843.98888387213-0.4379622086070.5280237454650.05469576476280.0939841819459-0.158011088386-0.0754624904542-0.02350961712290.146241453090.00617226160772-0.0332156469021-0.0311914509110.161541900075-0.01801861305280.004758907747410.154085461581-0.00507298049150.14772067549114.6535.73424.048
21.732088877310.1473754189570.1829112213760.7943507790330.1679824016030.328380332026-0.02601567705710.1480094778860.0940997157748-0.09022805220910.0302167826219-0.0252856731077-0.02718752846990.0165164662165-0.00547220059350.1824105878920.003564223884770.006512564408380.1727635783990.006533367338810.15647539866824.48115.8723.644
30.2134134953140.0955557541495-0.6511264253780.1213799757560.2454981267917.412444487440.0374876177446-0.0655976575539-0.01288649613440.04556917171890.02149883795560.0279128938228-0.21315519304-0.0538366975296-0.05407569801710.1809799742650.001705721431910.003835600578810.191656720526-0.000942614410320.1841550211240.14715.17849.871
42.07493870259-1.7057012882-3.151601276662.612552474111.17338363756.44681860677-0.232579165544-0.729154070796-0.466564922351-0.430078646776-0.188011587941-1.44810163506-0.04615098364280.8949921948250.4358347354010.2707637564190.02257370053330.04090263547110.2937635616580.08063166854850.38690754883526.2264.85743.339
54.23251157906-0.6218224959785.257331308161.19868690773-0.3183343304126.86205652686-0.008666515461650.0500169504159-0.3236783130150.0206686831318-0.01234128701940.0788001508355-0.0116310399423-0.0670921152724-0.0002880455820.2029033340340.01598455715380.03041117511990.1604470376040.01376420540730.1995329201488.232.41445.656
64.359906947855.34945067445-2.455809793047.23976447887-2.249734015614.124978191860.07952091341090.3380299189490.164619758060.3281216125240.1604571129551.254307427050.172769343724-0.829346200848-0.2026048299040.195741713706-0.04380198417040.04107752278150.3223861532440.06633989793820.469997238687-6.326-1.52844.049
79.191217444815.831459287-2.688665822395.25971097586-1.105084215331.699367386-0.2439833854020.0688985782444-0.205238958163-0.1449918027590.081706211236-0.007735191895850.186771255541-0.04079989675820.1662591000250.223668037640.01301334194680.01117120200030.1807234817520.0262175344660.15782038210311.901-2.14640.692
85.025473294172.63842347259-3.297937356097.525884822871.176200894213.54146470112-0.4273025795290.0149019651758-0.593573274848-0.8477189637090.0548264047232-0.2262363604311.369068865560.3089666527810.339275420320.3616788484960.02529742867510.06276669981740.199506563462-0.01486532694720.3732657779528.103-11.36239.393
96.534296519233.608146649122.512816353114.38030095694-2.621787805927.698302123330.122457597048-0.01243156507960.194587671501-0.029413494664-0.1624754116130.2379011174680.267608937168-0.2153535072580.07933690561640.1836006618340.0344706513610.02693703248120.156457382655-0.02438816405760.15962734965317.8159.16134.555
106.008942375225.13835032561-4.331749318544.62566165407-3.949323965694.14701818533-0.2987693766360.217145130457-0.106691243359-0.460706699820.263875247150.3138854938390.328828323572-0.1925510763470.02398123496630.225276218066-0.00454296693488-0.005278788685830.15286386485-0.01793489109460.2648151763967.402-1.68237.723
114.599452533925.17445718947-5.291241027745.82586714613-5.963756916756.11466960877-0.108302416253-1.25939093-1.041502270490.294023444650.4876725380570.4074464012220.476638951149-0.760584193798-0.4826762710230.382798611267-0.03534085384740.04206261286970.3990079154910.08710441657650.472891027887-2.6-10.74451.376
126.150023146013.74832695995-2.81369923574.30016424487-1.372206005921.40631905443-0.138550660895-0.438166864473-0.5771853297540.127356678318-0.0987455311959-0.1904591525780.1874055982350.1877709995690.2148194571390.2689636495310.04843333680570.03393134637350.257931982810.1026287169850.32036927366417.862-5.54846.548
132.81537154161-3.96214341067-1.720247135516.510005015050.2970960460176.12250291494-0.316982483344-0.54290157551-0.4704959213530.7914685931360.009379602771240.2547762235120.194498922966-0.1105088672150.2642714093850.328299608978-0.02928331030240.06515311652610.2825868911750.05762642047960.2517643300875.37-2.01651.398
146.573470790391.413740687850.9550827697036.845008975660.9790572682954.00987532679-0.01528213354350.2874370691320.15856226747-0.214819089143-0.0352418246443-0.8799373741050.05995427578510.1354788769230.02642371234710.245623762814-0.006452226180510.02068700797790.2013581975580.01717596590190.26476964026321.63614.32716.926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:56 )A1 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:174 )A57 - 174
3X-RAY DIFFRACTION3( CHAIN A AND RESID 175:274 )A175 - 274
4X-RAY DIFFRACTION4( CHAIN B AND RESID 0:5 )B0 - 5
5X-RAY DIFFRACTION5( CHAIN B AND RESID 6:11 )B6 - 11
6X-RAY DIFFRACTION6( CHAIN B AND RESID 12:19 )B12 - 19
7X-RAY DIFFRACTION7( CHAIN B AND RESID 20:41 )B20 - 41
8X-RAY DIFFRACTION8( CHAIN B AND RESID 42:51 )B42 - 51
9X-RAY DIFFRACTION9( CHAIN B AND RESID 52:61 )B52 - 61
10X-RAY DIFFRACTION10( CHAIN B AND RESID 62:71 )B62 - 71
11X-RAY DIFFRACTION11( CHAIN B AND RESID 72:77 )B72 - 77
12X-RAY DIFFRACTION12( CHAIN B AND RESID 78:90 )B78 - 90
13X-RAY DIFFRACTION13( CHAIN B AND RESID 91:99 )B91 - 99
14X-RAY DIFFRACTION14( CHAIN P AND RESID 1:6 )P1 - 6

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