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- EMDB-6808: Class1 cryoEM structure of human M-type phospholipase A2 receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-6808
TitleClass1 cryoEM structure of human M-type phospholipase A2 receptor
Map data
Sample
  • Organelle or cellular component: The ectodomain of human M-type phospholipase A2 receptor
    • Other: PLA2R1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsDong Y / Cao L / Shi X / Tang H / He Y
CitationJournal: J Mol Biol / Year: 2017
Title: Structure of Human M-type Phospholipase A2 Receptor Revealed by Cryo-Electron Microscopy.
Authors: Yue Dong / Longxing Cao / Hua Tang / Xiangyi Shi / Yongning He /
Abstract: M-type phospholipase A2 receptor (M-PLA2R) is a member of the mannose receptor family and known as the receptor of secretory phospholipase A2s. It has also been identified as the major autoantigen of ...M-type phospholipase A2 receptor (M-PLA2R) is a member of the mannose receptor family and known as the receptor of secretory phospholipase A2s. It has also been identified as the major autoantigen of idiopathic membranous nephropathy, one of the most common causes for nephrotic syndrome in adults. Here we determine the structure of human M-PLA2R ectodomain by cryo-electron microscopy. The results show that the ectodomain has high internal flexibility and forms a compact dual-ring-shaped conformation at acidic pH and adopts extended conformations at basic pH. The inter-domain interactions of human M-PLA2R are explored by the binding studies with individual domains, showing the mechanism of the conformational change. In addition, the biochemical data suggest that mouse M-PLA2R recognizes mouse secretory phospholipase A2-G1B only at physiological or basic pH, rather than at acidic pH. These results suggest that the pH-dependent conformational change might play important roles in the functional activities of M-PLA2R such as ligand binding and release, and may also be relevant to the immunogenicity in membranous nephropathy.
History
DepositionAug 5, 2017-
Header (metadata) releaseMay 30, 2018-
Map releaseMay 30, 2018-
UpdateMay 30, 2018-
Current statusMay 30, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6808.png

Downloads & links

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Map

FileDownload / File: emd_6808.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.3 Å
Density
Contour LevelBy AUTHOR: 0.0322 / Movie #1: 0.0322
Minimum - Maximum-0.014687012 - 0.10327889
Average (Standard dev.)0.0023663102 (±0.014224088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 110.399994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z110.400110.400110.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
D min/max/mean-0.0150.1030.002

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Supplemental data

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Sample components

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Entire : The ectodomain of human M-type phospholipase A2 receptor

EntireName: The ectodomain of human M-type phospholipase A2 receptor
Components
  • Organelle or cellular component: The ectodomain of human M-type phospholipase A2 receptor
    • Other: PLA2R1

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Supramolecule #1: The ectodomain of human M-type phospholipase A2 receptor

SupramoleculeName: The ectodomain of human M-type phospholipase A2 receptor
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 180 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: PLA2R1

MacromoleculeName: PLA2R1 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MLLSPSLLLL LLLGAPRGCA EGVAAALTPE RLLEWQDKGI FVIQSESLKK CIQAGKSVLT LENCKQANKH MLWKWVSNH GLFNIGGSGC LGLNFSAPEQ PLSLYECDST LVSLRWRCNR KMITGPLQYS VQVAHDNTVV A SRKYIHKW ISYGSGGGDI CEYLHKDLHT ...String:
MLLSPSLLLL LLLGAPRGCA EGVAAALTPE RLLEWQDKGI FVIQSESLKK CIQAGKSVLT LENCKQANKH MLWKWVSNH GLFNIGGSGC LGLNFSAPEQ PLSLYECDST LVSLRWRCNR KMITGPLQYS VQVAHDNTVV A SRKYIHKW ISYGSGGGDI CEYLHKDLHT IKGNTHGMPC MFPFQYNHQW HHECTREGRE DDLLWCATTS RY ERDEKWG FCPDPTSAEV GCDTIWEKDL NSHICYQFNL LSSLSWSEAH SSCQMQGGTL LSITDETEEN FIR EHMSSK TVEVWMGLNQ LDEHAGWQWS DGTPLNYLNW SPEVNFEPFV EDHCGTFSSF MPSAWRSRDC ESTL PYICK KYLNHIDHEI VEKDAWKYYA THCEPGWNPY NRNCYKLQKE EKTWHEALRS CQADNSALID ITSLA EVEF LVTLLGDENA SETWIGLSSN KIPVSFEWSN DSSVIFTNWH TLEPHIFPNR SQLCVSAEQS EGHWKV KNC EERLFYICKK AGHVLSDAES GCQEGWERHG GFCYKIDTVL RSFDQASSGY YCPPALVTIT NRFEQAF IT SLISSVVKMK DSYFWIALQD QNDTGEYTWK PVGQKPEPVQ YTHWNTHQPR YSGGCVAMRG RHPLGRWE V KHCRHFKAMS LCKQPVENQE KAEYEERWPF HPCYLDWESE PGLASCFKVF HSEKVLMKRT WREAEAFCE EFGAHLASFA HIEEENFVNE LLHSKFNWTE ERQFWIGFNK RNPLNAGSWE WSDRTPVVSS FLDNTYFGED ARNCAVYKA NKTLLPLHCG SKREWICKIP RDVKPKIPFW YQYDVPWLFY QDAEYLFHTF ASEWLNFEFV C SWLHSDLL TIHSAHEQEF IHSKIKALSK YGASWWIGLQ EERANDEFRW RDGTPVIYQN WDTGRERTVN NQ SQRCGFI SSITGLWGSE ECSVSMPSIC KRKKVWLIEK KKDTPKQHGT CPKGWLYFNY KCLLLNIPKD PSS WKNWTH AQHFCAEEGG TLVAIESEVE QAFITMNLFG QTTSVWIGLQ NDDYETWLNG KPVVYSNWSP FDII NIPSH NTTEVQKHIP LCALLSSNPN FHFTGKWYFE DCGKEGYGFV CEKMQDTSGH GVNTSDMYPM PNTLE YGNR TYKIINANMT WYAAIKTCLM HKAQLVSITD QYHQSFLTVV LNRLGYAHWI GLFTTDNGLN FDWSDG TKS SFTFWKDEES SLLGDCVFAD SNGRWHSTAC ESFLQGAICH VPPETRQSEH PELCSETSIP WIKFKSN CY SFSTVLDSMS FEAAHEFCKK EGSNLLTIKD EAENAFLLEE LFAFGSSVQM VWLNAQFDGN NETIKWFD G TPTDQSNWGI RKPDTDYFKP HHCVALRIPE GLWQLSPCQE KKGFICKMEA DIHTAEALPE KG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
50.0 mMBIS-TRISBis-tris methaneBIS-TRISBis-tris methane
150.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 4-37 / Average exposure time: 0.2 sec. / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 142074
CTF correctionSoftware - Name: RELION (ver. 1.3)
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3)
Final reconstructionNumber classes used: 3 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 116486

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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