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- PDB-7srk: Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide ... -

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Basic information

Entry
Database: PDB / ID: 7srk
TitleSingle chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF
Components
  • RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
  • VHH
KeywordsIMMUNE SYSTEM / HLA / VHH / HPV / SCT
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of double-strand break repair via homologous recombination / regulation of DNA repair / 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 / replication fork / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / single-stranded DNA binding ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of double-strand break repair via homologous recombination / regulation of DNA repair / 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 / replication fork / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / single-stranded DNA binding / nuclear speck / immune response / external side of plasma membrane / signaling receptor binding / RNA binding / extracellular space / extracellular region
Similarity search - Function
RPA-related protein RADX / Family of unknown function (DUF5521) / 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 / : ...RPA-related protein RADX / Family of unknown function (DUF5521) / 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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / RPA-related protein RADX
Similarity search - Component
Biological speciesHomo sapiens (human)
Pongo pygmaeus (Bornean orangutan)
Lama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFinton, K.A.K. / Rupert, P.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Front Immunol / Year: 2023
Title: Effects of HLA single chain trimer design on peptide presentation and stability.
Authors: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.
History
DepositionNov 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH
C: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)119,7744
Polymers119,7744
Non-polymers00
Water1,49583
1
A: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH


Theoretical massNumber of molelcules
Total (without water)59,8872
Polymers59,8872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)59,8872
Polymers59,8872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.924, 76.072, 226.974
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

#1: Protein RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera / RPA-related and RAD51-antagonist / X-chromosome


Mass: 47350.027 Da / Num. of mol.: 2 / Mutation: Y108C, A163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pongo pygmaeus (Bornean orangutan)
Gene: RADX, CXorf57, B2M, HLA-A / Production host: Homo sapiens (human)
References: UniProt: Q6NSI4, UniProt: P16213, UniProt: A0A411J078
#2: Antibody VHH


Mass: 12536.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH 6.0, 200 mM KSCN, 18% Peg 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.83 Å / Num. obs: 42766 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 39.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.5
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 4213 / CC1/2: 0.906

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SQP

7sqp


Resolution: 2.5→29.83 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2599 2155 5.04 %
Rwork0.2285 40604 -
obs0.2301 42759 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7604 0 0 83 7687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00187796
X-RAY DIFFRACTIONf_angle_d0.457210604
X-RAY DIFFRACTIONf_chiral_restr0.03971121
X-RAY DIFFRACTIONf_plane_restr0.00441396
X-RAY DIFFRACTIONf_dihedral_angle_d4.36981086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.3491360.29832646X-RAY DIFFRACTION99.96
2.56-2.620.34491500.29382669X-RAY DIFFRACTION100
2.62-2.690.35461590.27612655X-RAY DIFFRACTION100
2.69-2.770.31531570.27862638X-RAY DIFFRACTION100
2.77-2.860.28211320.26332691X-RAY DIFFRACTION100
2.86-2.960.27641560.25992662X-RAY DIFFRACTION100
2.96-3.080.31891420.26122679X-RAY DIFFRACTION99.96
3.08-3.220.30571420.26562704X-RAY DIFFRACTION100
3.22-3.390.30941290.24782685X-RAY DIFFRACTION100
3.39-3.60.28891310.24292722X-RAY DIFFRACTION99.89
3.6-3.880.26491250.2232734X-RAY DIFFRACTION99.97
3.88-4.270.23221520.19852706X-RAY DIFFRACTION99.86
4.27-4.890.18111470.17132738X-RAY DIFFRACTION99.93
4.89-6.150.2231670.19832758X-RAY DIFFRACTION99.86
6.15-29.830.19731300.21082917X-RAY DIFFRACTION99.38
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)
11.691158608470.1534137093260.7848827838371.346988997780.3900189221593.51443060649-0.07566631848460.520623802947-0.00690076779994-0.2005834827780.02273550021160.0860124540248-0.1351862095020.1983482868830.1067375321860.190661222373-0.0261044596932-0.02888530787940.274434673659-0.02767047038190.1860878031763.22804239036-14.8840715434-31.3555356683
22.341675774870.151449139620.3366897788441.62974998740.3939831735171.693685655940.029870891102-0.116239531671-0.1431646067010.269416827815-0.0475409089873-0.05592608312550.1310124810840.09070636530670.02217343193730.278505216167-0.001325702159490.008254726042550.205214230852-0.06126761730070.24605774532910.2575644789-15.5491730349-11.7824742165
33.793570269280.2561723005392.112514168420.958050155821-0.7608868310863.77289545153-0.6487716200731.301170446210.483987367129-0.1986618819820.371196677525-0.161605895004-0.6346939248050.6842958661040.312418096430.535639555814-0.283384767982-0.08396408896790.7762316016550.1529679051560.32445394877719.085188716-4.05996588256-36.3874228726
42.354985409711.16578037379-0.5802877470692.5573349164-1.096663431495.679315807620.2356665785920.1544868155020.6658725167740.320241317788-0.2582280367010.569233785836-0.788081928086-0.279758452931-0.0211863324370.2424963833950.0910217622318-0.05055208043720.425123096235-0.06800246226890.554460632465-29.5579597411-16.9828644944-30.3871356786
55.191515214960.6812977996281.892742184894.96776532520.01900089561632.56632052034-0.2256976936491.193576548810.149164608777-1.21885467553-0.2201734154820.6996701476730.233295503044-0.485894792423-0.1207870826320.3706633421670.154654125433-0.1559915091360.778963301174-0.07193072154380.448924291234-25.8289231044-17.0679254484-41.250169044
62.892333646710.649284726866-1.049810970592.507747114730.5005795607310.896879183253-0.0945419787990.3120931430860.0833259723737-0.102529777859-0.0120427867620.420947563613-0.154495474129-0.2577096842630.09199474668190.2252822814680.0362643073738-0.07035566980530.408669447182-0.0811598842320.281288100018-19.9708268964-18.3938929102-32.7399972499
71.58217349882-1.026106082730.5329682370583.02790859872-1.683359825452.135201435520.0388601663530.224514646756-0.321243286296-0.181576339439-0.05979987139580.2975854560980.193694828952-0.115775670457-0.02838944866020.307285877605-0.0474222961150.03927251276690.347306406506-0.2350800398530.560694446721-12.0682592435-48.0141927-33.7538141294
81.168612374010.242836869702-0.049279179672.47769313305-0.8886934899581.8503657363-0.06307079571650.354426864445-0.438102259368-0.146641582528-0.09647222899690.05235952316120.252810137813-0.02414561222990.1264400237510.3378932830730.02573536932820.002855690505940.403643378831-0.2201000798270.480206150918-9.39547632269-43.9807601462-38.3280749661
91.152210010640.254681378409-0.1461242126832.47553909862-0.05981916812522.23998206064-0.01781765289380.0119666106429-0.1012504810140.1881056017980.0683297994401-0.233812758648-0.0638921819465-0.2110167640060.04245778669170.4162943592510.01475053202970.04004283489790.284554362718-0.1786293027210.556483182571-9.2024432564-42.8205205114-19.955747691
100.0288257858084-0.126255186439-0.4718515879263.73079262598-0.1170068996061.09231606113-0.0390355210932-0.189995949999-0.3452603307610.278924681004-0.00816408007724-0.1576237539760.3491157035210.004991118016810.02965307261680.517534937847-0.01359912914650.01414522105150.354205750825-0.05954142214220.711055162825-6.60717062683-59.525918975-14.8445671647
110.236749908399-1.05881702962-0.2679895632023.34440337490.06087322941753.26642831822-0.3953172980150.0939906265031-0.2251912477680.9467059832850.3597056609010.764840942266-0.321656196967-1.12594787814-0.1786267973220.4047721752150.004727762697430.2429331377550.734515444677-0.1376264350360.896004146811-28.0513199288-47.5052694231-18.4747734434
122.667034512730.8866380311841.594762442351.238147812640.4686367621171.134072687650.05376909066990.705555854194-0.150083470924-0.2391476498770.0319612332234-0.1210234234521.15518981008-0.9026560041730.04465260964480.710280659014-0.141278930951-0.001521416037080.648361685759-0.3048701729560.789961329743-27.3923172277-54.0336350013-48.1636040518
130.227589984949-0.4339874552050.0801101958610.498978834944-0.8054113799432.760731735670.4742207174570.5909717137-0.6203656104180.0959783073243-0.01226348645980.1432047238511.00723514853-1.05624908368-0.3061956218680.648361234588-0.206548911878-0.09561127714210.913333463932-0.4578860290160.943549686423-28.1636639033-55.9558542838-45.0615544524
144.51994567849-0.405103101165-3.545677048439.64436618285-1.914376030124.32222583291-0.4218293012370.579146977196-0.4441840490540.485759122860.595054949981-0.0984827378892-0.524277145851-1.16722819297-0.2853069580630.4296705205610.06431599653650.1095410214420.844059881033-0.2236295588240.6093857855311.7060503073-38.6385260242-58.6985214919
153.73418248743-0.8672316092173.516305994960.562797606722-0.6467903924283.453586442880.183319741947-0.886990149627-0.8416998035010.342913919456-0.522409893013-1.07537839812-0.7871577359561.531680239750.2135794520380.599909738931-0.322378678824-0.03477603937711.436608804730.1591599801731.2441525721227.0569219905-38.016022392-42.0948599397
167.331159139833.282781843873.061300527962.826156001242.969008238188.358667940960.180132759255-1.056143766310.324744382169-0.6397881891970.077902641494-0.348562209126-1.05733847036-0.494676596502-0.6506530644360.4952489464150.1127190087970.06128751423590.798810789558-0.01897394453690.61721689282414.2100321328-33.9296603032-55.090014136
175.26769117593-0.6888236360650.4499244612245.89304479610.1375382450695.71164100358-0.9452156824771.09390049928-0.6610287619670.209528304531-0.261457994885-0.235659609191-0.576487557297-0.11691488130.8910053397580.338966906129-0.1436812966740.1976232656430.565157750314-0.2725196284950.6020540642647.18363208704-37.0256207382-50.6170991616
182.157443914512.29236757758-1.122854171864.62785469634-0.5194784727011.940219127470.1837669591260.174516835139-1.370034468260.0566435696557-0.456176008193-0.6653157928870.410238739868-0.1020390641080.2723488071890.3917236746370.0135346306847-0.06501843167390.548557605992-0.0597056299280.862539170258.89205381755-44.2438958496-42.9141884705
197.90977114231-1.61079986063-0.5010288589976.45152472369-0.9074593163863.525573063770.133751682584-0.209963880102-0.01077434851370.4882196127850.169747466967-0.345069092824-0.2459290740720.256915627256-0.4395424673160.398892564232-0.00957044403456-0.00240671322460.543608564802-0.09461108245370.3527548761136.68738894646-32.0263978602-41.1529613056
202.32687926288-0.3911761166071.228232853466.6670229901-4.191648303358.01736499161-0.4618364648750.3217539302710.3839362592020.202797376733-0.272707458161-1.32007221006-0.145878737590.3574739319470.7173928709870.2663923045280.093889739948-0.009890189985370.657052298933-0.02970034769440.58483309550713.2462153782-30.2531944998-43.0709700275
213.4718586857-3.28917320272.543065711076.28230839053-2.972424456448.04270626405-0.761480673610.772132341337-0.0948738132504-0.241120351027-0.161367052325-0.977198051602-0.5108136020920.5735364412690.4619762786540.302580134351-0.1247270813140.174947184890.833973002414-0.1645509731790.52057086469813.6349264492-29.3843037581-51.6530605502
221.71574768465-1.458407400220.387478421281.23484985571-0.3696294438521.265942225080.674998804066-0.0837496535292-0.1455647969990.113165790255-0.244861789884-1.388720160820.1811457887340.528310821264-0.3877557224230.306868479660.0571619262608-0.3671675666070.714485444989-0.0807304909151.6605407947821.6970186394-39.9112486281-37.4003111415
234.181706484180.7755378982951.031907505591.90952049113-0.9283150370525.020607391440.3816127951540.602645111263-0.486026400388-0.674821379416-0.388749351545-0.686508988060.3175639744420.248711896352-0.2553545316410.4756410318830.04156087798530.08033171292560.762513752883-0.3874824187350.5221747533865.7109821184-40.6155823607-52.4903848554
241.42559147672-2.26229448907-0.02574682095765.127740532341.407967628742.94789622415-0.643838643229-0.1100311473620.354669543524-0.262670001736-0.956359128645-0.240013640213-0.0813647015113-0.4980029149551.073027591560.2851261811360.5295748750470.3340722446410.706719098160.1048539445831.1251084353422.6633029739-43.63982588-45.521218659
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 107 )AA1 - 1071 - 92
22chain 'A' and (resid 108 through 305 )AA108 - 30593 - 268
33chain 'A' and (resid 306 through 415 )AA306 - 415269 - 373
44chain 'B' and (resid 3 through 19 )BB3 - 191 - 17
55chain 'B' and (resid 20 through 32 )BB20 - 3218 - 30
66chain 'B' and (resid 33 through 117 )BB33 - 11731 - 115
77chain 'C' and (resid 1 through 43 )CC1 - 431 - 27
88chain 'C' and (resid 44 through 155 )CC44 - 15528 - 119
99chain 'C' and (resid 156 through 199 )CC156 - 199120 - 163
1010chain 'C' and (resid 200 through 305 )CC200 - 305164 - 269
1111chain 'C' and (resid 306 through 328 )CC306 - 328270 - 292
1212chain 'C' and (resid 329 through 362 )CC329 - 362293 - 326
1313chain 'C' and (resid 363 through 417 )CC363 - 417327 - 381
1414chain 'D' and (resid 3 through 9 )DD3 - 91 - 7
1515chain 'D' and (resid 10 through 19 )DD10 - 198 - 17
1616chain 'D' and (resid 20 through 29 )DD20 - 2918 - 27
1717chain 'D' and (resid 30 through 41 )DD30 - 4128 - 39
1818chain 'D' and (resid 42 through 53 )DD42 - 5340 - 51
1919chain 'D' and (resid 54 through 65 )DD54 - 6552 - 63
2020chain 'D' and (resid 66 through 74 )DD66 - 7464 - 72
2121chain 'D' and (resid 75 through 84 )DD75 - 8473 - 82
2222chain 'D' and (resid 85 through 92 )DD85 - 9283 - 90
2323chain 'D' and (resid 93 through 111 )DD93 - 11191 - 109
2424chain 'D' and (resid 112 through 116 )DD112 - 116110 - 114

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