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- EMDB-20850: Focused map of type 3 IP3 receptor N-terminal domain revealing th... -

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Basic information

Entry
Database: EMDB / ID: EMD-20850
TitleFocused map of type 3 IP3 receptor N-terminal domain revealing the presence of a self-binding peptide
Map data
Sample
  • Complex: inositol 1,4,5-triphosphate receptor, type 3
    • Protein or peptide: inositol 1,4,5-triphosphate receptor, type 3
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsAzumaya CM / Linton EA / Risener CJ / Nakagawa T / Karakas E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseDK020593 United States
CitationJournal: J Biol Chem / Year: 2020
Title: Cryo-EM structure of human type-3 inositol triphosphate receptor reveals the presence of a self-binding peptide that acts as an antagonist.
Authors: Caleigh M Azumaya / Emily A Linton / Caitlin J Risener / Terunaga Nakagawa / Erkan Karakas /
Abstract: Calcium-mediated signaling through inositol 1,4,5-triphosphate receptors (IPRs) is essential for the regulation of numerous physiological processes, including fertilization, muscle contraction, ...Calcium-mediated signaling through inositol 1,4,5-triphosphate receptors (IPRs) is essential for the regulation of numerous physiological processes, including fertilization, muscle contraction, apoptosis, secretion, and synaptic plasticity. Deregulation of IPRs leads to pathological calcium signaling and is implicated in many common diseases, including cancer and neurodegenerative, autoimmune, and metabolic diseases. Revealing the mechanism of activation and inhibition of this ion channel will be critical to an improved understanding of the biological processes that are controlled by IPRs. Here, we report structural findings of the human type-3 IPR (IPR-3) obtained by cryo-EM (at an overall resolution of 3.8 Å), revealing an unanticipated regulatory mechanism where a loop distantly located in the primary sequence occupies the IP-binding site and competitively inhibits IP binding. We propose that this inhibitory mechanism must differ qualitatively among IPR subtypes because of their diverse loop sequences, potentially serving as a key molecular determinant of subtype-specific calcium signaling in IPRs. In summary, our structural characterization of human IPR-3 provides critical insights into the mechanistic function of IPRs and into subtype-specific regulation of these important calcium-regulatory channels.
History
DepositionOct 20, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.85
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.85
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20850.png

Downloads & links

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Map

FileDownload / File: emd_20850.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.247 Å
Density
Contour LevelBy AUTHOR: 1.85 / Movie #1: 1.85
Minimum - Maximum-7.2958636 - 14.292088
Average (Standard dev.)-0.028875573 (±0.40946305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 423.97998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2471.2471.247
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z423.980423.980423.980
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-7.29614.292-0.029

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Supplemental data

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Additional map: unsharpened map

Fileemd_20850_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_20850_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_20850_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_20850_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : inositol 1,4,5-triphosphate receptor, type 3

EntireName: inositol 1,4,5-triphosphate receptor, type 3
Components
  • Complex: inositol 1,4,5-triphosphate receptor, type 3
    • Protein or peptide: inositol 1,4,5-triphosphate receptor, type 3

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Supramolecule #1: inositol 1,4,5-triphosphate receptor, type 3

SupramoleculeName: inositol 1,4,5-triphosphate receptor, type 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: inositol 1,4,5-triphosphate receptor, type 3

MacromoleculeName: inositol 1,4,5-triphosphate receptor, type 3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSFLHIGDI VSLYAEGSVN GFISTLGLVD DRCVVEPAAG DLDNPPKKFR DCLFKVCPMN RYSAQKQYWK AKQTKQDKEK IADVVLLQKL QHAAQMEQKQ NDTENKKVHG DVVKYGSVIQ LLHMKSNKYL TVNKRLPALL EKNAMRVTLD ATGNEGSWLF IQPFWKLRSN ...String:
MSSFLHIGDI VSLYAEGSVN GFISTLGLVD DRCVVEPAAG DLDNPPKKFR DCLFKVCPMN RYSAQKQYWK AKQTKQDKEK IADVVLLQKL QHAAQMEQKQ NDTENKKVHG DVVKYGSVIQ LLHMKSNKYL TVNKRLPALL EKNAMRVTLD ATGNEGSWLF IQPFWKLRSN GDNVVVGDKV ILNPVNAGQP LHASNYELSD NAGCKEVNSV NCNTSWKINL FMQFRDHLEE VLKGGDVVRL FHAEQEKFLT CDEYKGKLQV FLRTTLRQSA TSATSSNALW EVEVVHHDPC RGGAGHWNGL YRFKHLATGN YLAAEENPSY KGDASDPKAA GMGAQGRTGR RNAGEKIKYC LVAVPHGNDI ASLFELDPTT LQKTDSFVPR NSYVRLRHLC TNTWIQSTNV PIDIEEERPI RLMLGTCPTK EDKEAFAIVS VPVSEIRDLD FANDASSMLA SAVEKLNEGF ISQNDRRFVI QLLEDLVFFV SDVPNNGQNV LDIMVTKPNR ERQKLMREQN ILKQVFGILK APFREKGGEG PLVRLEELSD QKNAPYQHMF RLCYRVLRHS QEDYRKNQEH IAKQFGMMQS QIGYDILAED TITALLHNNR KLLEKHITKT EVETFVSLVR KNREPRFLDY LSDLCVSNHI AIPVTQELIC KCVLDPKNSD ILIRTELRPV KEMAQSHEYL SIEYSEEEVW LTWTDKNNEH HEKSVRQLAQ EARAGNAHDE NVLSYYRYQL KLFARMCLDR QYLAIDEISQ QLGVDLIFLC MADEMLPFDL RASFCHLMLH VHVDRDPQEL VTPVKFARLW TEIPTAITIK DYDSNLNASR DDKKNKFANT MEFVEDYLNN VVSEAVPFAN EEKNKLTFEV VSLAHNLIYF GFYSFSELLR LTRTLLGIID CVQGPPAMLQ AYEDPGGKNV RRSIQGVGHM MSTMVLSRKQ SVFSAPSLSA GASAAEPLDR SKFEENEDIV VMETKLKILE ILQFILNVRL DYRISYLLSV FKKEFVEVFP MQDSGADGTA PAFDSTTANM NLDRIGEQAE AMFGVGKTSS MLEVDDEGGR MFLRVLIHLT MHDYAPLVSG ALQLLFKHFS QRQEAMHTFK QVQLLISAQD VENYKVIKSE LDRLRTMVEK SELWVDKKGS GKGEEVEAGA AKDKKERPTD EEGFLHPPGE KSSENYQIVK GILERLNKMC GVGEQMRKKQ QRLLKNMDAH KVMLDLLQIP YDKGDAKMME ILRYTHQFLQ KFCAGNPGNQ ALLHKHLHLF LTPGLLEAET MQHIFLNNYQ LCSEISEPVL QHFVHLLATH GRHVQYLDFL HTVIKAEGKY VKKCQDMIMT ELTNAGDDVV VFYNDKASLA HLLDMMKAAR DGVEDHSPLM YHISLVDLLA ACAEGKNVYT EIKCTSLLPL EDVVSVVTHE DCITEVKMAY VNFVNHCYVD TEVEMKEIYT SNHIWTLFEN FTLDMARVCS KREKRVADPT LEKYVLSVVL DTINAFFSSP FSENSTSLQT HQTIVVQLLQ STTRLLECPW LQQQHKGSVE ACIRTLAMVA KGRAILLPMD LDAHISSMLS SGASCAAAAQ RNASSYKATT RAFPRVTPTA NQWDYKNIIE KLQDIITALE ERLKPLVQAE LSVLVDVLHW PELLFLEGSE AYQRCESGGF LSKLIQHTKD LMESEEKLCI KVLRTLQQML LKKTKYGDRG NQLRKMLLQN YLQNRKSTSR GDLPDPIGTG LDPDWSAIAA TQCRLDKEGA TKLVCDLITS TKNEKIFQES IGLAIHLLDG GNTEIQKSFH NLMMSDKKSE RFFKVLHDRM KRAQQETKST VAVNMNDLGS QPHEDREPVD PTTKGRVASF SIPGSSSRYS LGPSLRRGHE VSERVQSSEM GTSVLIMQPI LRFLQLLCEN HNRDLQNFLR CQNNKTNYNL VCETLQFLDI MCGSTTGGLG LLGLYINEDN VGLVIQTLET LTEYCQGPCH ENQTCIVTHE SNGIDIITAL ILNDISPLCK YRMDLVLQLK DNASKLLLAL MESRHDSENA ERILISLRPQ ELVDVIKKAY LQEEERENSE VSPREVGHNI YILALQLSRH NKQLQHLLKP VKRIQEEEAE GISSMLSLNN KQLSQMLKSS APAQEEEEDP LAYYENHTSQ IEIVRQDRSM EQIVFPVPGI CQFLTEETKH RLFTTTEQDE QGSKVSDFFD QSSFLHNEME WQRKLRSMPL IYWFSRRMTL WGSISFNLAV FINIIIAFFY PYMEGASTGV LDSPLISLLF WILICFSIAA LFTKRYSIRP LIVALILRSI YYLGIGPTLN ILGALNLTNK IVFVVSFVGN RGTFIRGYKA MVMDMEFLYH VGYILTSVLG LFAHELFYSI LLFDLIYREE TLFNVIKSVT RNGRSILLTA LLALILVYLF SIVGFLFLKD DFILEVDRLP NNHSTASPLG MPHGAAAFVD TCSGDKMDCV SGLSVPEVLE EDRELDSTER ACDTLLMCIV TVMNHGLRNG GGVGDILRKP SKDESLFPAR VVYDLLFFFI VIIIVLNLIF GVIIDTFADL RSEKQKKEEI LKTTCFICGL ERDKFDNKTV SFEEHIKLEH NMWNYLYFIV LVRVKNKTDY TGPESYVAQM IKNKNLDWFP RMRAMSLVSN EGEGEQNEIR ILQDKLNSTM KLVSHLTAQL NELKEQMTEQ RKRRQRLGFV DVQNCISRGE NLYFQSAWSH PQFEKGGGSG GGSGGSAWSH PQFEK

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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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationName
200.0 mMNaCl
20.0 mMTris-HCl
1.0 mMEDTA
2.0 mMTCEP
0.005 %Lauryl maltose neopentyl glycol
0.005 %GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: The grid was blotted for 3 seconds at force 1.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 31000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

6369

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 56767
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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