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- PDB-7tue: Crystal structure of Tapasin in complex with HLA-B*44:05 (T73C) -

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Basic information

Entry
Database: PDB / ID: 7tue
TitleCrystal structure of Tapasin in complex with HLA-B*44:05 (T73C)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Tapasin
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


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP2 binding / TAP1 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP2 binding / TAP1 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / unfolded protein binding / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / regulation of gene expression / protein refolding / protein-containing complex assembly / early endosome membrane / protein homotetramerization / amyloid fibril formation / molecular adaptor activity / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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
Tapasin / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Tapasin / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tapasin / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Tapasin
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)88,4233
Polymers88,4233
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.866, 116.866, 131.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#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 Tapasin / TPN / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 44739.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): S2 / References: UniProt: O15533
#3: 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
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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.0M AmSO4, 0.1M Tris / PH range: 6.5-8.5

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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: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→80.12 Å / Num. obs: 18395 / % possible obs: 99.83 % / Redundancy: 5.8 % / CC1/2: 0.94 / CC star: 0.985 / Rmerge(I) obs: 0.3367 / Rpim(I) all: 0.1488 / Rrim(I) all: 0.3687 / Net I/σ(I): 3.22
Reflection shellResolution: 3.1→3.216 Å / Redundancy: 6 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1831 / CC1/2: 0.587 / CC star: 0.86 / Rpim(I) all: 0.435 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8U

3f8u


Resolution: 3.1→80.12 Å / Cross valid method: FREE R-VALUE / σ(F): 242.33 / Phase error: 28.661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3088 920 5 %
Rwork0.2856 17472 -
obs0.2982 18392 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.76 Å2
Refinement stepCycle: LAST / Resolution: 3.1→80.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 0 0 5630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235796
X-RAY DIFFRACTIONf_angle_d0.63777918
X-RAY DIFFRACTIONf_chiral_restr0.0431845
X-RAY DIFFRACTIONf_plane_restr0.00561046
X-RAY DIFFRACTIONf_dihedral_angle_d17.02212121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.270.35141310.32182501X-RAY DIFFRACTION94.63
3.27-3.470.37331300.28562472X-RAY DIFFRACTION94.97
3.47-3.740.27531310.27372489X-RAY DIFFRACTION94.82
3.74-4.120.26861300.27982478X-RAY DIFFRACTION94.98
4.12-4.710.32021320.26462516X-RAY DIFFRACTION95.02
4.72-5.940.31161310.28932486X-RAY DIFFRACTION94.78
5.94-80.120.36971340.3372531X-RAY DIFFRACTION94.62
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)
10.309250655876-0.1194337035680.2075519259240.0604742206009-0.0586308395690.1718116414690.1899932273050.0194350846042-0.0503146973812-0.0868390719617-0.009349827781960.0476889333250.1203965832370.043143982362-0.003585714116510.510259378618-0.124659017507-0.1945699871790.2234402918180.1003055590870.643349762598-46.3829.492-42.022
20.0186237794453-0.010184183858-0.01184259531960.01099354834770.02248529938250.0611476488842-0.016631441374-0.0124855190604-0.04678171900520.1113047473620.0706427691739-0.06155778031610.04422928276340.027792827152-0.003394394644450.83099356881-0.0380411291111-0.1431614577270.251775482718-0.1465350775240.829128745109-51.85721.568-31.175
30.007890387089350.0115424811922-0.01590311821380.0287676159449-0.04546834766610.07258597766780.000179075698248-0.0210524894233-0.071928707830.0737014183148-0.01041350183070.0410821628045-0.0189248521107-0.00524516927959-0.034267441870.823520313977-0.190418371279-0.06066518968850.226562903329-0.02231967539140.840745053787-42.81719.471-43.867
40.00101772758947-0.006105893255550.001732833955420.04105292741910.01960962328270.1591686268480.0009038276029510.06295535201730.06090421875180.05855288619040.06503332883090.0353647751598-0.130475880276-0.0568468779245-0.00992405904630.719327243024-0.1723799640640.2810157245030.5907576480760.2475002481160.729545253417-43.04629.107-37.858
53.1183792172E-6-0.00010249088664-0.000120158174245-8.13195426319E-5-4.77236078877E-5-0.000124429371945-0.01340430619780.0186105973978-0.0074247597766-0.00834033909994-0.0388600330517-0.015021458660.0377784428420.007660817463-0.05661997966350.4689808227050.1710262240460.08211927399190.560528551026-0.2057379211450.358533667578-41.80337.794-28.654
60.203766700102-9.57805956511E-5-0.2041566168970.0614253329853-0.05410826989310.2510833602-0.07993128569310.005353628995350.0507181693167-0.0225660187253-0.00187567723635-0.02867216463-0.03712236620270.0285417424757-0.1776290841110.264314861264-0.0930486441867-0.1016183612470.6051900349930.1630460451030.210729659444-35.33823.561-39.72
70.02941258490240.0848550662821-0.01847420728110.221620362609-0.08877051510020.112043393457-0.174540796145-0.0437977025842-0.112676953372-0.0139592160356-0.01194899997910.2150997349980.1002112471050.0459916167813-0.3134015141260.389368373785-0.01317912519190.04464682822590.1419256340280.2588898602980.728376274304-25.64562.349-2.565
80.1812725157010.001034928214740.2665506504290.153295861881-0.1961338398050.642296335149-0.2499551836850.320015194431-0.108088269190.157603468416-0.188353014164-0.0468731023334-0.0466025369754-0.255091182572-0.3058947686510.189848323921-0.1017295195010.1846271093860.376331272369-0.01082053773480.635649425014-30.7253.8837.391
90.00284155309118-0.0146130549517-0.002856733405660.07710339393310.0431359783145-0.002878513292570.07097666972670.220656917452-0.234887122045-0.0231850814835-0.0586609554765-0.0331679344480.04783777154090.05996985129150.05998888792910.1341211546270.104837336517-0.1774467808410.482509704688-0.2140777386031.15694258603-25.56642.89315.612
100.340196562486-0.1554561382230.2227825430060.158929154316-0.2634025774480.4391929852140.3401859251910.153742195812-0.137919842857-0.1667200559040.05612937491060.05939436563490.4423851212260.004816985182220.3085891053530.526955867122-0.0219283648924-0.4760953115980.2418282039730.1330064761561.07459453851-25.66233.406-1.965
110.07488356794750.117441369965-0.004401460320630.1669293009730.06276818760450.5165346474190.1867532402290.009926528165520.194991018319-0.1080286339190.1641836864760.156521924173-0.0930206554638-0.236760008840.1122350117070.42839304142-0.2055715378990.05120727860260.2398865712060.2022141766321.09235960398-20.21621.019-37.907
120.3648605600430.0707323149265-0.06438592653060.282025461506-0.1433583073950.0565402024184-0.137640837076-0.339045894274-0.5818715719-0.108842387932-0.146403794038-0.08155715573540.2463916632540.109376258747-0.0152285299550.3295391488520.1660751397190.12157549710.302015937521-0.04632611335070.717147557339-55.07533.962-11.62
130.03572007181640.028365963918-0.02759791739160.0102679681514-0.0164154029970.0137754187696-0.199663310073-0.116243618112-0.005495557067040.132342472906-0.211627806743-0.145153920824-0.148226931856-0.1564892422550.000142603672110.3274691377420.00906571819744-0.08119706915580.486706169470.005858401598150.946107253565-47.60533.3682.186
140.01687183679230.00426071491197-0.009125031187610.0166433921713-0.0301531302010.03022236512320.04336985601570.02077980020920.1931775822230.150393931757-0.003337589244890.0794561964811-0.01709338408550.1545099860220.002445220970390.400090380873-0.145737705404-0.1417603099080.361664717937-0.0286719210980.501939938277-40.96610.996-15.06
150.07088518669110.1662495380650.2899210532560.3775102720910.6661460762651.16713544520.0875437127829-0.0220011517585-0.152371147655-0.09722017434720.395964286188-0.3240505022890.0332395463220.1663747089330.2267463503510.2991260264940.00971845917660.04540270728390.2465696470250.1539015052961.11929060658-31.48714.692-12.494
160.00147416014669-0.004193485705710.003282750085060.0118641937267-0.01257277139460.0133920794554-0.150974684072-0.0415619470053-0.0648839060834-0.1588898802990.0290079744714-0.07206711250040.126013497799-0.04235090568220.0001089888000720.810695834129-0.03260999283630.1156550545850.4287254719510.04588155976170.806915047411-38.99723.826-28.499
170.02296975856320.0205105338211-0.03147324709720.08470459203050.03597233682750.104656872791-0.07189695727610.02076660778790.140136938560.0939066399058-0.0135476954675-0.0829469069071-0.011926322685-0.0437776123586-0.01920897909730.337332666545-0.0169272789626-0.1450777598840.387134687180.1735664625810.311386787262-39.20710.241-44.278
180.04078237381720.03032426302090.02272275311040.0419258160434-0.01659351355830.06869379044790.0649340507483-0.09939064910590.0429581999770.005456780653450.02030809006730.02655818417120.01464140391290.02042113217150.01994992892180.192319543251-0.0608209800739-0.03196356930440.5909717615410.3157509786390.621400271877-43.14418.028-35.165
190.07863804597020.08400354661580.01151166088660.106194370124-0.006375590298180.02216361245080.00857977429851-0.0449638278970.0186365719965-0.0281255966389-0.00528795926422-0.03028206082-0.03819422970720.0142090651687-0.04235441369610.743438502358-0.29653935133-0.1012515388160.420392214629-0.1670378485750.775707842938-48.03830.104-23.009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 36:46 )B36 - 46
2X-RAY DIFFRACTION2( CHAIN B AND RESID 47:64 )B47 - 64
3X-RAY DIFFRACTION3( CHAIN B AND RESID 65:77 )B65 - 77
4X-RAY DIFFRACTION4( CHAIN B AND RESID 78:83 )B78 - 83
5X-RAY DIFFRACTION5( CHAIN B AND RESID 84:90 )B84 - 90
6X-RAY DIFFRACTION6( CHAIN B AND RESID 91:98 )B91 - 98
7X-RAY DIFFRACTION7( CHAIN D AND RESID 1:69 )D1 - 69
8X-RAY DIFFRACTION8( CHAIN D AND RESID 70:155 )D70 - 155
9X-RAY DIFFRACTION9( CHAIN D AND RESID 156:238 )D156 - 238
10X-RAY DIFFRACTION10( CHAIN D AND RESID 239:277 )D239 - 277
11X-RAY DIFFRACTION11( CHAIN D AND RESID 278:381 )D278 - 381
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1:103 )A1 - 103
13X-RAY DIFFRACTION13( CHAIN A AND RESID 104:174 )A104 - 174
14X-RAY DIFFRACTION14( CHAIN A AND RESID 175:197 )A175 - 197
15X-RAY DIFFRACTION15( CHAIN A AND RESID 198:274 )A198 - 274
16X-RAY DIFFRACTION16( CHAIN B AND RESID 3:11 )B3 - 11
17X-RAY DIFFRACTION17( CHAIN B AND RESID 12:19 )B12 - 19
18X-RAY DIFFRACTION18( CHAIN B AND RESID 20:28 )B20 - 28
19X-RAY DIFFRACTION19( CHAIN B AND RESID 29:35 )B29 - 35

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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