+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14077 | ||||||||||||||||||
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Title | Structure of PLA2R at pH 6.2 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Membranous nephropathy / IMMUNE SYSTEM | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of arachidonate secretion / negative regulation of phospholipase A2 activity / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / positive regulation of DNA damage response, signal transduction by p53 class mediator / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / positive regulation of podocyte apoptotic process ...negative regulation of arachidonate secretion / negative regulation of phospholipase A2 activity / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / positive regulation of DNA damage response, signal transduction by p53 class mediator / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / positive regulation of podocyte apoptotic process / positive regulation of arachidonate secretion / oxidative stress-induced premature senescence / phospholipase binding / replicative senescence / reactive oxygen species metabolic process / receptor-mediated endocytosis / positive regulation of cytokine production / signaling receptor activity / carbohydrate binding / receptor complex / cell surface / extracellular region / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Lockhart-Cairns MP / Rhoden SJ / Fresquet M / Jowitt TA / Briggs DC / Baldock C / Brenchley P / Lennon R | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Structure of PLA2R reveals presentation of the dominant membranous nephropathy epitope and an immunogenic patch. Authors: Maryline Fresquet / Michael P Lockhart-Cairns / Samuel J Rhoden / Thomas A Jowitt / David C Briggs / Clair Baldock / Paul E Brenchley / Rachel Lennon / Abstract: Membranous nephropathy is an autoimmune kidney disease caused by autoantibodies targeting antigens present on glomerular podocytes, instigating a cascade leading to glomerular injury. The most ...Membranous nephropathy is an autoimmune kidney disease caused by autoantibodies targeting antigens present on glomerular podocytes, instigating a cascade leading to glomerular injury. The most prevalent circulating autoantibodies in membranous nephropathy are against phospholipase A2 receptor (PLA2R), a cell surface receptor. The dominant epitope in PLA2R is located within the cysteine-rich domain, yet high-resolution structure-based mapping is lacking. In this study, we define the key nonredundant amino acids in the dominant epitope of PLA2R involved in autoantibody binding. We further describe two essential regions within the dominant epitope and spacer requirements for a synthetic peptide of the epitope for drug discovery. In addition, using cryo-electron microscopy, we have determined the high-resolution structure of PLA2R to 3.4 Å resolution, which shows that the dominant epitope and key residues within the cysteine-rich domain are accessible at the cell surface. In addition, the structure of PLA2R not only suggests a different orientation of domains but also implicates a unique immunogenic signature in PLA2R responsible for inducing autoantibody formation and recognition. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14077.map.gz | 32.2 MB | EMDB map data format | |
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Header (meta data) | emd-14077-v30.xml emd-14077.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
Images | emd_14077.png | 93.6 KB | ||
Filedesc metadata | emd-14077.cif.gz | 6.6 KB | ||
Others | emd_14077_additional_1.map.gz emd_14077_additional_2.map.gz emd_14077_half_map_1.map.gz emd_14077_half_map_2.map.gz | 60.3 MB 59.6 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14077 | HTTPS FTP |
-Validation report
Summary document | emd_14077_validation.pdf.gz | 753.6 KB | Display | EMDB validaton report |
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Full document | emd_14077_full_validation.pdf.gz | 753.2 KB | Display | |
Data in XML | emd_14077_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_14077_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14077 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14077 | HTTPS FTP |
-Related structure data
Related structure data | 7qsrMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10915 (Title: CryoEM data of PLA2R at pH 6.2 with both 0 and 30 degree tilts. Data size: 2.1 TB Data #1: Unaligned multi-frame images of PLA2R at pH 6.2 with a 30 degree tilt. [micrographs - multiframe] Data #2: Unaligned multi-frame images of PLA2R at pH 6.2 with 0 degree tilt (not used in publication) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14077.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1672 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_14077_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_14077_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14077_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14077_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Secretory phospholipase A2 receptor
Entire | Name: Secretory phospholipase A2 receptor |
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Components |
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-Supramolecule #1: Secretory phospholipase A2 receptor
Supramolecule | Name: Secretory phospholipase A2 receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: Truncated protein produced in HEK293 EBNA cells and purified in pH 6.2 buffer. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: Secretory phospholipase A2 receptor
Macromolecule | Name: Secretory phospholipase A2 receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EGVAAALTPE RLLEWQDKGI FVIQSESLKK CIQAGKSVLT LENCKQANKH MLWKWVSNHG LFNIGGSGC LGLNFSAPEQ PLSLYECDST LVSLRWRCNR KMITGPLQYS VQVAHDNTVV A SRKYIHKW ISYGSGGGDI CEYLHKDLHT IKGNTHGMPC MFPFQYNHQW ...String: EGVAAALTPE RLLEWQDKGI FVIQSESLKK CIQAGKSVLT LENCKQANKH MLWKWVSNHG LFNIGGSGC LGLNFSAPEQ PLSLYECDST LVSLRWRCNR KMITGPLQYS VQVAHDNTVV A SRKYIHKW ISYGSGGGDI CEYLHKDLHT IKGNTHGMPC MFPFQYNHQW HHECTREGRE DD LLWCATT SRYERDEKWG FCPDPTSAEV GCDTIWEKDL NSHICYQFNL LSSLSWSEAH SSC QMQGGT LLSITDETEE NFIREHMSSK TVEVWMGLNQ LDEHAGWQWS DGTPLNYLNW SPEV NFEPF VEDHCGTFSS FMPSAWRSRD CESTLPYICK KYLNHIDHEI VEKDAWKYYA THCEP GWNP YNRNCYKLQK EEKTWHEALR SCQADNSALI DITSLAEVEF LVTLLGDENA SETWIG LSS NKIPVSFEWS NDSSVIFTNW HTLEPHIFPN RSQLCVSAEQ SEGHWKVKNC EERLFYI CK KAGHVLSDAE SGCQEGWERH GGFCYKIDTV LRSFDQASSG YYCPPALVTI TNRFEQAF I TSLISSVVKM KDSYFWIALQ DQNDTGEYTW KPVGQKPEPV QYTHWNTHQP RYSGGCVAM RGRHPLGRWE VKHCRHFKAM SLCKQPVENQ EKAEYEERWP FHPCYLDWES EPGLASCFKV FHSEKVLMK RTWREAEAFC EEFGAHLASF AHIEEENFVN ELLHSKFNWT EERQFWIGFN K RNPLNAGS WEWSDRTPVV SSFLDNTYFG EDARNCAVYK ANKTLLPLHC GSKREWICKI PR DVKPKIP FWYQYDVPWL FYQDAEYLFH TFASEWLNFE FVCSWLHSDL LTIHSAHEQE FIH SKIKAL SKYGASWWIG LQEERANDEF RWRDGTPVIY QNWDTGRERT VNNQSQRCGF ISSI TGLWG SEECSVSMPS ICKRKKVWLI EKKKDTPKQH GTCPKGWLYF NYKCLLLNIP KDPSS WKNW THAQHFCAEE GGTLVAIESE VEQAFITMNL FGQTTSVWIG LQNDDYETWL NGKPVV YSN WSPFDIINIP SHNTTEVQKH IPLCALLSSN PNFHFTGKWY FEDCGKEGYG FVCEKMQ DT SGHGVNTSDM YPMPNTLEYG NRTYKIINAN MTWYAAIKTC LMHKAQLVSI TDQYHQSF L TVVLNRLGYA HWIGLFTTDN GLNFDWSDGT KSSFTFWKDE ESSLLGDCVF ADSNGRWHS TACESFLQGA ICHVPPETRQ SEHPELCSET SIPWIKFKSN CYSFSTVLDS MSFEAAHEFC KKEGSNLLT IKDEAENAFL LEELFAFGSS VQMVWLNAQF DGNNETIKWF DGTPTDQSNW G IRKPDTDY FKPHHCVALR IPEGLWQLSP CQEKKGFICK MEADIHTAEA LPEKGPSHS UniProtKB: UNIPROTKB: Q1301 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.33 mg/mL | |||||||||
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Buffer | pH: 6.2 Component:
Details: 10 mM Bis-Tris, pH 6.2, 150 mM NaCl | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Sample were applied to the grid in the chamber and blotted for 3 seconds.. | |||||||||
Details | Sample was purified from secreted mammalian media with Ni affinity. The sample was further purified with SEC and buffer exchanged to pH 6.2. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | 30 degree tilt of stage |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 42.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7qsr: |