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- EMDB-9247: Structure of full-length IP3R1 channel in ligand-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-9247
TitleStructure of full-length IP3R1 channel in ligand-bound state
Map dataCryo-EM densty map of IP3R1 in a ligand-bound state
Sample
  • Complex: Inositol 1,4,5-trisphosphate receptor
    • Protein or peptide: inositol 1,4,5-trisphosphate receptor
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsFan G / Baker MR / Wang Z / Seryshev AB / Ludtke SJ / Baker ML / Serysheva II
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072804 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR063255 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS106968 United States
American Heart Association16GRNT2972000 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Science Foundation (NSF, United States)DBI-1356306 United States
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM reveals ligand induced allostery underlying InsPR channel gating.
Authors: Guizhen Fan / Mariah R Baker / Zhao Wang / Alexander B Seryshev / Steven J Ludtke / Matthew L Baker / Irina I Serysheva /
Abstract: Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the ...Inositol-1,4,5-trisphosphate receptors (InsPRs) are cation channels that mobilize Ca from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsPR activation is the coupled interplay between binding of InsP and Ca that switches the ion conduction pathway between closed and open states to enable the passage of Ca through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsPR1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca and adenophostin A (AdA), a structural mimetic of InsP and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsPR1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsPR channel.
History
DepositionOct 22, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseDec 5, 2018-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9247.png

Downloads & links

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Map

FileDownload / File: emd_9247.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM densty map of IP3R1 in a ligand-bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 200 pix.
= 252. Å		1.26 Å/pix.
x 200 pix.
= 252. Å		1.26 Å/pix.
x 200 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.4814746 - 1.8334695
Average (Standard dev.)0.035191 (±0.1394396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-1.4811.8330.035

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Supplemental data

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Sample components

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Entire : Inositol 1,4,5-trisphosphate receptor

EntireName: Inositol 1,4,5-trisphosphate receptor
Components
  • Complex: Inositol 1,4,5-trisphosphate receptor
    • Protein or peptide: inositol 1,4,5-trisphosphate receptor

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Supramolecule #1: Inositol 1,4,5-trisphosphate receptor

SupramoleculeName: Inositol 1,4,5-trisphosphate receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: tetrameric assembly
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Brain / Tissue: Cerebellum / Organelle: endoplasmic reticulum / Location in cell: membrane
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: inositol 1,4,5-trisphosphate receptor

MacromoleculeName: inositol 1,4,5-trisphosphate receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: MSDKMSSFLH IGDICSLYAE GSTNGFISTL GLVDDRCVVQ PEAGDLNNPP KKFRDCLFKL CPMNRYSAQK QFWKAAKPG ANSTTDAVLL NKLHHAADLE KKQNETENRK LLGTVIQYGN VIQLLHLKSN KYLTVNKRLP A LLEKNAMR VTLDEAGNEG SWFYIQPFYK ...String:
MSDKMSSFLH IGDICSLYAE GSTNGFISTL GLVDDRCVVQ PEAGDLNNPP KKFRDCLFKL CPMNRYSAQK QFWKAAKPG ANSTTDAVLL NKLHHAADLE KKQNETENRK LLGTVIQYGN VIQLLHLKSN KYLTVNKRLP A LLEKNAMR VTLDEAGNEG SWFYIQPFYK LRSIGDSVVI GDKVVLNPVN AGQPLHASSH QLVDNPGCNE VN SVNCNTS WKIVLFMKWS DNKDDILKGG DVVRLFHAEQ EKFLTCDEHR KKQHVFLRTT GRQSATSATS SKA LWEVEV VQHDPCRGGA GYWNSLFRFK HLATGHYLAA EVDPDFEEEC LEFQPSVDPD QDASRSRLRN AQEK MVYSL VSVPEGNDIS SIFELDPTTL RGGDSLVPRN SYVRLRHLCT NTWVHSTNIP IDKEEEKPVM LKIGT SPLK EDKEAFAIVP VSPAEVRDLD FANDASKVLG SIAGKLEKGT ITQNERRSVT KLLEDLVYFV TGGTNS GQD VLEVVFSKPN RERQKLMREQ NILKQIFKLL QAPFTDCGDG PMLRLEELGD QRHAPFRHIC RLCYRVL RH SQQDYRKNQE YIAKQFGFMQ KQIGYDVLAE DTITALLHNN RKLLEKHITA AEIDTFVSLV RKNREPRF L DYLSDLCVSM NKSIPVTQEL ICKAVLNPTN ADILIETKLV LSRFEFEGVS TGENALEAGE DEEEVWLFW RDSNKEIRSK SVRELAQDAK EGQKEDRDVL SYYRYQLNLF ARMCLDRQYL AINEISGQLD VDLILRCMSD ENLPYDLRA SFCRLMLHMH VDRDPQEQVT PVKYARLWSE IPSEIAIDDY DSSGASKDEI KERFAQTMEF V EEYLRDVV CQRFPFSDKE KNKLTFEVVN LARNLIYFGF YNFSDLLRLT KILLAILDCV HVTTIFPISK MT KGEENKG SNVMRSIHGV GELMTQVVLR GGGFLPMTPM AAAPEGNVKQ AEPEKEDIMV MDTKLKIIEI LQF ILNVRL DYRISCLLCI FKREFDESNS QSSETSSGNS SQEGPSNVPG ALDFEHIEEQ AEGIFGGSEE NTPL DLDDH GGRTFLRVLL HLTMHDYPPL VSGALQLLFR HFSQRQEVLQ AFKQVQLLVT SQDVDNYKQI KQDLD QLRS IVEKSELWVY KGQGPDEPMD GASGENEHKK TEEGTSKPLK HESTSSYNYR VVKEILIRLS KLCVQE SAS VRKSRKQQQR LLRNMGAHAV VLELLQIPYE KAEDTKMQEI MRLAHEFLQN FCAGNQQNQA LLHKHIN LF LNPGILEAVT MQHIFMNNFQ LCSEINERVV QHFVHCIETH GRNVQYIKFL QTIVKAEGKF IKKCQDMV M AELVNSGEDV LVFYNDRASF QTLIQMMRSE RDRMDENSPL FMYHIHLVEL LAVCTEGKNV YTEIKCNSL LPLDDIVRVV THEDCIPEVK IAYINFLNHC YVDTEVEMKE IYTSNHMWKL FENFLVDICR ACNNTSDRKH ADSVLEKYV TEIVMSIVTT FFSSPFSDQS TTLQTRQPVF VQLLQGVFRV YHCNWLMPSQ KASVESCIRV L SDVAKSRA IAIPVDLDSQ VNNLFLKSHN IVQKTAMNWR LSARNAARRD SVLAASRDYR NIIERLQDIV SA LEDRLRP LVQAELSVLV DVLHRPELLF PENTDARRKC ESGGFICKLI KHTKQLLEEN EEKLCIKVLQ TLR EMMTKD RGYGEKQISI DELENAELPQ PPEAENSTEQ ELEPSPPLRQ LEDHKRGEAL RQILVNRYYG NIRP SGRRE SLTSFGNGPL SPGGPSKPGG GGGGPGSGST SRGEMSLAEV QCHLDKEGAS NLVIDLIMNA SSDRV FHES ILLAIALLEG GNTTIQHSFF CRLTEDKKSE KFFKVFYDRM KVAQQEIKAT VTVNTSDLGN KKKDDE VDR DAPSRKKAKE PTTQITEEVR DQLLEASAAT RKAFTTFRRE ADPDDHYQSG EGTQATTDKA KDDLEMS AV ITIMQPILRF LQLLCENHNR DLQNFLRCQN NKTNYNLVCE TLQFLDCICG STTGGLGLLG LYINEKNV A LINQTLESLT EYCQGPCHEN QNCIATHESN GIDIITALIL NDINPLGKKR MDLVLELKNN ASKLLLAIM ESRHDSENAE RILYNMRPKE LVEVIKKAYM QGEVEFEDGE NGEDGAASPR NVGHNIYILA HQLARHNKEL QTMLKPGGQ VDGDEALEFY AKHTAQIEIV RLDRTMEQIV FPVPSICEFL TKESKLRIYY TTERDEQGSK I NDFFLRSE DLFNEMNWQK KLRAQPVLYW CARNMSFWSS ISFNLAVLMN LLVAFFYPFK GVRGGTLEPH WS GLLWTAM LISLAIVIAL PKPHGIRALI ASTILRLIFS VGLQPTLFLL GAFNVCNKII FLMSFVGNCG TFT RGYRAM VLDVEFLYHL LYLLICAMGL FVHEFFYSLL LFDLVYREET LLNVIKSVTR NGRPIILTAA LALI LVYLF SIVGYLFFKD DFILEVDRLP NETAGPETGE SLANDFLYSD VCRVETGENC TSPAPKEELL PVEET EQDK EHTCETLLMC IVTVLSHGLR SGGGVGDVLR KPSKEEPLFA ARVIYDLLFF FMVIIIVLNL IFGVII DTF ADLRSEKQKK EEILKTTCFI CGLERDKFDN KTVTFEEHIK EEHNMWHYLC FIVLVKVKDS TEYTGPE SY VAEMIRERNL DWFPRMRAMS LVSSDSEGEQ NELRNLQEKL ESTMKLVTNL SGQLSELKDQ MTEQRKQK Q RIGLLGHPPH MNVNPQQPA

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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

BufferpH: 7.4
Details: 50 mM Tris-HCl buffer (pH 7.4), 150 mM NaCl, 1 mM DTT, 0.4% CHAPS,100 nM of AdA, 300 nM of Ca2+, protease inhibitors
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unavailable
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details0.1 mg/ml

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 93.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-17 / Number real images: 14686 / Average exposure time: 0.2 sec. / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 191646
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

6369

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 50903
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)

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