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- PDB-7sqp: Single chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YM... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7sqp
TitleSingle chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YMLDLQPETTDL
Components
  • Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
  • VHH
KeywordsIMMUNE SYSTEM / HLA / VHH / HPV / SCT
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation / viral process ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation / viral process / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / recycling endosome membrane / phagocytic vesicle membrane / early endosome membrane / DNA-binding transcription factor binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / DNA-binding transcription factor activity / protein domain specific binding / DNA-templated transcription / host cell nucleus / cell surface / DNA binding / zinc ion binding / extracellular region
Similarity search - Function
Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...Papillomavirus E7 / E7 protein, Early protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
MHC class I antigen / Protein E7 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHuman papillomavirus type 16
Pongo pygmaeus (Bornean orangutan)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 5, 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: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH
C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)120,9714
Polymers120,9714
Non-polymers00
Water1,946108
1
A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH


Theoretical massNumber of molelcules
Total (without water)60,4852
Polymers60,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)60,4852
Polymers60,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.979, 117.979, 262.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera


Mass: 47948.629 Da / Num. of mol.: 2 / Mutation: Y108C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16, (gene. exp.) Pongo pygmaeus (Bornean orangutan), (gene. exp.) Homo sapiens (human)
Gene: E7, B2M, HLA-A / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P03129, UniProt: P16213, UniProt: A0A678ZGP6
#2: Antibody VHH


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 4.03 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 200 mM NH4Citrate, 20.0% PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 61220 / % possible obs: 97.93 % / Redundancy: 9.3 % / Biso Wilson estimate: 56.23 Å2 / CC1/2: 0.997 / Net I/σ(I): 33.9
Reflection shellResolution: 2.53→2.62 Å / Num. unique obs: 5234 / CC1/2: 0.997

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Processing

SoftwareName: CrysalisPro / Version: 1.19.1_4122 / Classification: data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JF1
Resolution: 2.53→48.96 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 3089 5.05 %
Rwork0.2387 58084 -
obs0.2398 61173 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.03 Å2
Refinement stepCycle: LAST / Resolution: 2.53→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7503 0 0 108 7611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167698
X-RAY DIFFRACTIONf_angle_d0.486810497
X-RAY DIFFRACTIONf_chiral_restr0.03951133
X-RAY DIFFRACTIONf_plane_restr0.0051363
X-RAY DIFFRACTIONf_dihedral_angle_d4.30371089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.570.3856960.34762030X-RAY DIFFRACTION76.15
2.57-2.620.35811250.30262451X-RAY DIFFRACTION92.76
2.62-2.660.28761310.29312504X-RAY DIFFRACTION94.95
2.66-2.710.35461580.28942532X-RAY DIFFRACTION96.42
2.71-2.760.34971530.28672577X-RAY DIFFRACTION97.36
2.76-2.820.31531450.28862633X-RAY DIFFRACTION99.14
2.82-2.880.2841650.2992629X-RAY DIFFRACTION99.43
2.88-2.950.3771250.30582659X-RAY DIFFRACTION99.82
2.95-3.020.36531390.32412661X-RAY DIFFRACTION99.82
3.02-3.10.38341320.29282697X-RAY DIFFRACTION99.89
3.1-3.190.30681420.26512638X-RAY DIFFRACTION99.93
3.19-3.30.25431460.26112677X-RAY DIFFRACTION99.96
3.3-3.410.27271360.2542672X-RAY DIFFRACTION99.93
3.41-3.550.27461490.25522697X-RAY DIFFRACTION99.96
3.55-3.710.23371290.25122694X-RAY DIFFRACTION100
3.71-3.910.24161410.21612688X-RAY DIFFRACTION99.96
3.91-4.150.22741380.20552712X-RAY DIFFRACTION100
4.15-4.470.20941510.19482715X-RAY DIFFRACTION99.97
4.47-4.920.20931500.18562726X-RAY DIFFRACTION99.93
4.92-5.630.1971320.20492775X-RAY DIFFRACTION99.97
5.63-7.090.25071310.23722804X-RAY DIFFRACTION100
7.09-48.960.26891750.23582913X-RAY DIFFRACTION98.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.93950675322-0.910826834539-0.8490382617470.8445292693810.5337288804130.252383550259-0.434299046926-0.473565778578-0.3928567548260.1999467965780.2197278754620.0648220521710.04212855353530.2736577889160.162911676310.5455853990240.1389989073570.08977607950870.5331951610540.1328541944680.382728721494-13.630754641-31.5321084171-24.1887711126
22.93778710689-0.737830211211-0.6520685434161.386442617090.3254191208521.47320937723-0.1384646364360.235512389613-0.3082573405160.0877604591860.003477769401940.222069327044-0.187571471155-0.1071499865260.1002525003550.4787195791110.02438512356070.06952948514520.436054887605-0.01107960333540.469382369463-4.38476404069-37.9897511582-39.1193994853
30.9496559462460.05331189268470.03857521026141.227256314120.04173795551661.51857781275-0.3702513031030.47250671113-0.87839011923-0.177852215931-0.07997740244140.3626937019310.934417571022-0.008566278987510.2656042106390.9425077388980.3164996630090.3433547327380.8357771403220.1507497699420.883535565605-11.8316270182-49.5521507352-10.7886647237
47.04862877899-1.169186999420.6110308661863.541687621912.372929862341.91417174669-0.0875092404862-0.3504673734550.0376012051237-0.07332377613730.3957400251160.1803503985420.4883271836760.060636253788-0.1419369991340.5973966512290.06645510867920.02097744577810.602053627837-0.01482768666320.393439060882-40.0716659738-15.8848539745-14.496370553
51.820036436810.859356959854-0.3106663175971.946223246540.006026733709551.84654266624-0.436598497666-0.2836238330211.288378492090.1318941813220.7006073569930.331637905232-0.842457513750.09668026820030.1925926018030.3367597615410.0974914572023-0.02760831506540.519540231650.1573928347850.569703836089-38.7579982784-5.95401387737-27.4034255282
60.707289068242-0.355194940690.8733077718560.181473115346-0.4408860051221.07522637784-0.475527530218-0.5747717863540.05534782918210.6342832881890.0427540165713-0.2022374144310.4175507778280.115436679465-0.07974690583270.8758149473070.207224045844-0.07036795046881.571173865060.007200928407560.893430370565-33.3179353919-14.828038743-3.96217807112
72.71392083577-0.311599708962-0.3910991378332.45188309552-0.9480054632261.06757643809-0.287931084105-0.09570044304680.0193753712946-0.4363848525640.09986137036630.05166060281490.2460448413380.2550441639340.02896050704460.4864418586020.0632682280013-0.01356386595540.4806412403970.02893407606080.452495905141-30.5011930699-18.3408817435-24.3428952982
82.016845126020.1910972469361.400469480012.12099064971-0.7198700671113.13922582530.187272213425-0.01960947178430.6711117863560.005161034603140.249328101664-0.312245696828-0.09854524702120.5365256228520.03773369283910.4934365866740.0438234119817-0.09393703182510.564144177387-0.02815106706630.583815792874-25.2548755656-8.83825915215-22.7554191167
92.6667791742-0.00391164016835-1.699742077933.33738286697-0.1828597828091.127400808820.478566135177-0.8828443022510.9850368775240.6183874196930.3916833349180.236815863765-0.1955236265250.419272588387-0.0749092896580.5342706972770.0573983427590.1022438056110.643916101484-0.144870177620.696981243709-32.9986339775-6.48896430701-16.3628447099
102.5523785709-0.2096644037790.5701917337841.31316082702-0.6172421428871.2420089735-0.163753999749-0.3669225597210.113972020810.03525421891510.3276238495710.269031189141-0.0535954936978-0.03592551959774.43153584375E-50.5574171058730.139690778637-0.008715984616560.4701179241960.003326224917250.423658975805-33.1462652969-16.8427144577-22.7169988022
115.283260383260.400639158016-0.003890319788054.998145876790.7470344963760.137465032815-0.5746699912550.8614987931670.661874918441-0.9939672570920.134523300399-0.008939699280410.277848111899-9.9611267238E-5-0.06220036818620.439002732041-0.011380560417-0.09317220482680.6540335099170.1258289542550.504753858935-40.8797558659-11.0554467588-34.0504607107
122.934329530480.9796346850091.114191410391.284614372760.5407522812891.06193984038-0.3482025082030.2114994254970.477018321753-0.1463336755360.1241495095410.149589553188-0.023048389310.1310593662810.1777987813350.445968423398-0.0780304458886-0.07654078981490.3892404366650.05864646414830.407946588374-11.698838223330.772530801-42.2052251535
134.139508240351.377755215060.7808564919381.402276702130.4531420945131.69799473789-0.253882450339-0.5821283497280.686060814975-0.0222309780869-0.02756536196630.3086057313530.0819162830452-0.1480879632760.1888323105950.4484722634020.040688306183-0.09460122694590.459688591315-0.094910592560.550319244939-2.1080620450438.2911490505-27.3592755167
140.493946347631-0.608845114567-0.468931759521.214213174030.03607222433950.58234551717-0.9564035978410.5391565765221.57546493167-0.5334602233560.5828608455470.423641061431-0.6205634930950.1737079623670.02689089690760.985510608947-0.453834938114-0.6157655054280.6843640648360.5376824581031.36607412171-10.237780894148.8160567758-54.7110469459
156.344780387670.791114165272-0.3601297129944.022065013642.023057723641.10989238814-0.0276167305764-0.00852244373349-0.2743354627960.1033386743980.1393233026570.623768475689-0.335045950815-0.162579566743-0.1571747037570.501159235715-0.05093574408740.0097252429230.579132153562-0.04900412628910.603759407288-37.899619539614.0625539631-50.27274997
164.97303576206-1.979652585811.600347718342.72790780123-0.1292473039540.66504612166-0.426469677562-0.268815183355-0.02705048858710.497954024602-0.08691522934190.2163741541470.294387002118-0.146741422580.08806899527430.6169539781810.03919514505410.1141010478170.5367347096510.06743684927830.598634201314-37.59942538435.11898332003-29.5514604855
171.21331215128-0.335916822343-0.02319040944732.12450644113-1.596853210245.09859471872-0.4168289419270.690899204254-0.201253073815-0.7208411582460.8647778274080.4433820166930.4202163252230.8119073314760.08948852617550.473450423152-0.1603821042850.01605047615950.5844397748810.00835969373480.568838525679-34.96924508256.65487136543-43.7161857422
180.451082870629-0.7378485297680.1350189616333.1700074188-1.067737535090.404549697928-0.5779802455870.959839580070.24607909656-0.609840808769-0.0505736833224-0.246017116042-0.1764174235290.2146043922240.03131749577620.897833319652-0.551489172960.01188647334181.67805221924-0.1815476873280.782677530861-32.10439737112.8041294713-60.1394839612
191.866210466180.373595641588-0.6127908236531.57340169676-0.1465213755272.22938996373-0.2416331406860.1601229461180.112718631718-0.3720303593850.007612589348380.117139299035-0.0856971058823-0.3540868684930.1199988386410.47669970346-0.1443330855610.06008952760270.4560257930930.004024573192520.548983548193-28.782247675715.3896593192-44.5259481547
202.46576025974-0.6043946270650.8683626656675.994856338960.5236385660921.53399428876-0.376014917649-0.531679473797-0.02891311782821.104544769140.07435607409430.110023994769-0.0402478288101-0.3594453590730.1850953515140.641035724426-0.02717874795260.03719765247740.5064817360140.009592758567210.477060310975-27.988619722419.9688464914-37.776893756
210.988805337403-0.248161179366-1.348635613571.49050131052-0.6216882306394.504761608680.0410110531435-0.248627228854-0.394808330135-0.07183332971150.0980824806137-0.5467742743570.4884682598220.09581261226860.08488255578440.41771031526-0.04386869810640.1262823428510.4630188132210.0141101877120.566374947551-22.88061196198.36309335466-41.3989807565
223.340009503770.3651999017592.106853754374.27823987214-0.7719022737313.728593825110.1089438608450.315702726452-0.0355783945513-0.5809837918080.63287154242-0.182371412344-0.1316745025660.39259351636-0.07540542824480.408217549725-0.06208986612020.009595815064280.5164255951920.002299304423350.487755754563-30.61991465435.24125003138-47.0312191503
231.88429873537-2.68217363985-0.7443364084664.902520984350.9372317885390.403888076038-0.0796331027268-0.131500156991-0.2011908218690.94769878825-0.00975959797745-0.247835508585-0.1381124573250.843468289038-0.09225337909940.7265325838980.07187379521460.1475463532820.603053545520.05086994075430.688143227936-30.80289693019.51763638934-27.966388857
242.027392515790.137118566773-2.01091090610.781514674138-0.2880065798443.578074901210.07974419392160.425562262618-0.201067414914-0.2144496341080.1523802400930.6099566343920.0734425187622-0.5531790823890.1728093591080.526980538414-0.0662073482150.08907638269190.385235105340.04720338970380.426464817202-32.209830458616.8072845183-42.5512611454
252.799227991820.388824283102-1.476915415961.4221287446-0.369113389772.49972775442-0.2403107280710.2387506356440.395407210489-0.04877970043160.2714775257140.402917990192-0.319377334065-0.09963332881970.1369689817410.480716722418-0.1440573681090.00930036083830.494029355785-0.01418967449730.536507634291-32.87495956517.6847524921-45.3624212804
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 155 )AA1 - 1551 - 124
22chain 'A' and (resid 156 through 340 )AA156 - 340125 - 309
33chain 'A' and (resid 341 through 417 )AA341 - 417310 - 382
44chain 'B' and (resid 3 through 9 )BB3 - 91 - 7
55chain 'B' and (resid 10 through 26 )BB10 - 268 - 24
66chain 'B' and (resid 27 through 32 )BB27 - 3225 - 30
77chain 'B' and (resid 33 through 53 )BB33 - 5331 - 51
88chain 'B' and (resid 54 through 74 )BB54 - 7452 - 72
99chain 'B' and (resid 75 through 84 )BB75 - 8473 - 82
1010chain 'B' and (resid 85 through 111 )BB85 - 11183 - 109
1111chain 'B' and (resid 112 through 118 )BB112 - 118110 - 116
1212chain 'C' and (resid 1 through 155 )CC1 - 1551 - 123
1313chain 'C' and (resid 156 through 341 )CC156 - 341124 - 307
1414chain 'C' and (resid 342 through 417 )CC342 - 417308 - 380
1515chain 'D' and (resid 3 through 9 )DD3 - 91 - 7
1616chain 'D' and (resid 10 through 19 )DD10 - 198 - 17
1717chain 'D' and (resid 20 through 26 )DD20 - 2618 - 24
1818chain 'D' and (resid 27 through 32 )DD27 - 3225 - 30
1919chain 'D' and (resid 33 through 41 )DD33 - 4131 - 39
2020chain 'D' and (resid 42 through 53 )DD42 - 5340 - 51
2121chain 'D' and (resid 54 through 74 )DD54 - 7452 - 72
2222chain 'D' and (resid 75 through 84 )DD75 - 8473 - 82
2323chain 'D' and (resid 85 through 92 )DD85 - 9283 - 90
2424chain 'D' and (resid 93 through 100 )DD93 - 10091 - 98
2525chain 'D' and (resid 101 through 117 )DD101 - 11799 - 115

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