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- EMDB-7987: Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-7987
TitleClass 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Map dataClass 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Sample
  • Organelle or cellular component: human type 3 inositol 1,4,5-trisphosphate receptor
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 3
  • Ligand: ZINC ION
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
Function / homology
Function and homology information


sensory perception of bitter taste / DAG and IP3 signaling / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / platelet dense tubular network membrane / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / PLC beta mediated events ...sensory perception of bitter taste / DAG and IP3 signaling / sensory perception of umami taste / inositol 1,3,4,5 tetrakisphosphate binding / inositol 1,4,5-trisphosphate-gated calcium channel activity / sensory perception of sweet taste / platelet dense tubular network membrane / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / PLC beta mediated events / inositol hexakisphosphate binding / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / CLEC7A (Dectin-1) induces NFAT activation / intracellularly gated calcium channel activity / cytoplasmic side of endoplasmic reticulum membrane / brush border / Role of phospholipids in phagocytosis / calcium ion homeostasis / release of sequestered calcium ion into cytosol / Ion homeostasis / phosphatidylinositol binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / secretory granule membrane / sarcoplasmic reticulum / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / long-term synaptic potentiation / Regulation of insulin secretion / Sensory perception of sweet, bitter, and umami (glutamate) taste / memory / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / response to calcium ion / sensory perception of taste / apical part of cell / myelin sheath / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / receptor complex / G protein-coupled receptor signaling pathway / neuronal cell body / calcium ion binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif ...Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate receptor type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.47 Å
AuthorsHite RK / Paknejad N
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structural basis for the regulation of inositol trisphosphate receptors by Ca and IP.
Authors: Navid Paknejad / Richard K Hite /
Abstract: Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, ...Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IPRs are jointly activated by inositol trisphosphate (IP) and their permeant ion, Ca. At high concentrations, however, Ca inhibits activity, ensuring precise spatiotemporal control over intracellular Ca. Despite extensive characterization of IPR, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IPRs in ligand-bound and ligand-free states. Multiple IP-bound structures demonstrate that the large cytoplasmic domain provides a platform for propagation of long-range conformational changes to the ion-conduction gate. Structures in the presence of Ca reveal two Ca-binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IPR. These structures thus provide a mechanistic basis for beginning to understand the regulation of IPR.
History
DepositionJun 11, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseAug 1, 2018-
UpdateAug 1, 2018-
Current statusAug 1, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dr0
  • Surface level: 3.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7987.png

Downloads & links

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Map

FileDownload / File: emd_7987.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Voxel sizeX=Y=Z: 1.088 Å
Density
Contour LevelBy AUTHOR: 3.06 / Movie #1: 3.06
Minimum - Maximum-6.272461 - 11.857538999999999
Average (Standard dev.)-0.0055783093 (±0.5509331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z417.792417.792417.792
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-6.27211.858-0.006

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Supplemental data

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Sample components

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Entire : human type 3 inositol 1,4,5-trisphosphate receptor

EntireName: human type 3 inositol 1,4,5-trisphosphate receptor
Components
  • Organelle or cellular component: human type 3 inositol 1,4,5-trisphosphate receptor
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 3
  • Ligand: ZINC ION
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

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

SupramoleculeName: human type 3 inositol 1,4,5-trisphosphate receptor / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK 293S GnTi / Recombinant plasmid: BacMam

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Macromolecule #1: Inositol 1,4,5-trisphosphate receptor type 3

MacromoleculeName: Inositol 1,4,5-trisphosphate receptor type 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 304.488688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSEMSSFLHI GDIVSLYAEG SVNGFISTLG LVDDRCVVEP AAGDLDNPPK KFRDCLFKVC PMNRYSAQKQ YWKAKQTKQD KEKIADVVL LQKLQHAAQM EQKQNDTENK KVHGDVVKYG SVIQLLHMKS NKYLTVNKRL PALLEKNAMR VTLDATGNEG S WLFIQPFW ...String:
MSEMSSFLHI GDIVSLYAEG SVNGFISTLG LVDDRCVVEP AAGDLDNPPK KFRDCLFKVC PMNRYSAQKQ YWKAKQTKQD KEKIADVVL LQKLQHAAQM EQKQNDTENK KVHGDVVKYG SVIQLLHMKS NKYLTVNKRL PALLEKNAMR VTLDATGNEG S WLFIQPFW KLRSNGDNVV VGDKVILNPV NAGQPLHASN YELSDNAGCK EVNSVNCNTS WKINLFMQFR DHLEEVLKGG DV VRLFHAE QEKFLTCDEY KGKLQVFLRT TLRQSATSAT SSNALWEVEV VHHDPCRGGA GHWNGLYRFK HLATGNYLAA EEN PSYKGD ASDPKAAGMG AQGRTGRRNA GEKIKYCLVA VPHGNDIASL FELDPTTLQK TDSFVPRNSY VRLRHLCTNT WIQS TNVPI DIEEERPIRL MLGTCPTKED KEAFAIVSVP VSEIRDLDFA NDASSMLASA VEKLNEGFIS QNDRRFVIQL LEDLV FFVS DVPNNGQNVL DIMVTKPNRE RQKLMREQNI LKQVFGILKA PFREKGGEGP LVRLEELSDQ KNAPYQHMFR LCYRVL RHS QEDYRKNQEH IAKQFGMMQS QIGYDILAED TITALLHNNR KLLEKHITKT EVETFVSLVR KNREPRFLDY LSDLCVS NH IAIPVTQELI CKCVLDPKNS DILIRTELRP VKEMAQSHEY LSIEYSEEEV WLTWTDKNNE HHEKSVRQLA QEARAGNA H DENVLSYYRY QLKLFARMCL DRQYLAIDEI SQQLGVDLIF LCMADEMLPF DLRASFCHLM LHVHVDRDPQ ELVTPVKFA RLWTEIPTAI TIKDYDSNLN ASRDDKKNKF ANTMEFVEDY LNNVVSEAVP FANEEKNKLT FEVVSLAHNL IYFGFYSFSE LLRLTRTLL GIIDCVQGPP AMLQAYEDPG GKNVRRSIQG VGHMMSTMVL SRKQSVFSAP SLSAGASAAE PLDRSKFEEN E DIVVMETK LKILEILQFI LNVRLDYRIS YLLSVFKKEF VEVFPMQDSG ADGTAPAFDS TTANMNLDRI GEQAEAMFGV GK TSSMLEV DDEGGRMFLR VLIHLTMHDY APLVSGALQL LFKHFSQRQE AMHTFKQVQL LISAQDVENY KVIKSELDRL RTM VEKSEL WVDKKGSGKG EEVEAGAAKD KKERPTDEEG FLHPPGEKSS ENYQIVKGIL ERLNKMCGVG EQMRKKQQRL LKNM DAHKV MLDLLQIPYD KGDAKMMEIL RYTHQFLQKF CAGNPGNQAL LHKHLHLFLT PGLLEAETMQ HIFLNNYQLC SEISE PVLQ HFVHLLATHG RHVQYLDFLH TVIKAEGKYV KKCQDMIMTE LTNAGDDVVV FYNDKASLAH LLDMMKAARD GVEDHS PLM YHISLVDLLA ACAEGKNVYT EIKCTSLLPL EDVVSVVTHE DCITEVKMAY VNFVNHCYVD TEVEMKEIYT SNHIWTL FE NFTLDMARVC SKREKRVADP TLEKYVLSVV LDTINAFFSS PFSENSTSLQ THQTIVVQLL QSTTRLLECP WLQQQHKG S VEACIRTLAM VAKGRAILLP MDLDAHISSM LSSGASCAAA AQRNASSYKA TTRAFPRVTP TANQWDYKNI IEKLQDIIT ALEERLKPLV QAELSVLVDV LHWPELLFLE GSEAYQRCES GGFLSKLIQH TKDLMESEEK LCIKVLRTLQ QMLLKKTKYG DRGNQLRKM LLQNYLQNRK STSRGDLPDP IGTGLDPDWS AIAATQCRLD KEGATKLVCD LITSTKNEKI FQESIGLAIH L LDGGNTEI QKSFHNLMMS DKKSERFFKV LHDRMKRAQQ ETKSTVAVNM NDLGSQPHED REPVDPTTKG RVASFSIPGS SS RYSLGPS LRRGHEVSER VQSSEMGTSV LIMQPILRFL QLLCENHNRD LQNFLRCQNN KTNYNLVCET LQFLDIMCGS TTG GLGLLG LYINEDNVGL VIQTLETLTE YCQGPCHENQ TCIVTHESNG IDIITALILN DISPLCKYRM DLVLQLKDNA SKLL LALME SRHDSENAER ILISLRPQEL VDVIKKAYLQ EEERENSEVS PREVGHNIYI LALQLSRHNK QLQHLLKPVK RIQEE EAEG ISSMLSLNNK QLSQMLKSSA PAQEEEEDPL AYYENHTSQI EIVRQDRSME QIVFPVPGIC QFLTEETKHR LFTTTE QDE QGSKVSDFFD QSSFLHNEME WQRKLRSMPL IYWFSRRMTL WGSISFNLAV FINIIIAFFY PYMEGASTGV LDSPLIS LL FWILICFSIA ALFTKRYSIR PLIVALILRS IYYLGIGPTL NILGALNLTN KIVFVVSFVG NRGTFIRGYK AMVMDMEF L YHVGYILTSV LGLFAHELFY SILLFDLIYR EETLFNVIKS VTRNGRSILL TALLALILVY LFSIVGFLFL KDDFILEVD RLPNNHSTAS PLGMPHGAAA FVDTCSGDKM DCVSGLSVPE VLEEDRELDS TERACDTLLM CIVTVMNHGL RNGGGVGDIL RKPSKDESL FPARVVYDLL FFFIVIIIVL NLIFGVIIDT FADLRSEKQK KEEILKTTCF ICGLERDKFD NKTVSFEEHI K LEHNMWNY LYFIVLVRVK NKTDYTGPES YVAQMIKNKN LDWFPRMRAM SLVSNEGEGE QNEIRILQDK LNSTMKLVSH LT AQLNELK EQMTEQRKRR QRLGFVDVQN CISR

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

MacromoleculeName: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: I3P
Molecular weightTheoretical: 420.096 Da
Chemical component information

ChemComp-I3P:
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate

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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

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chlorideSodium Chlorid
50.0 mMTrisTris(hydroxymethyl)aminomethane hydrochloride
2.0 mMDTT1,4-Dithiothreitol
0.06 percentDigitoninDigitonin
5.0 mMEGTAethylene glycol-bis(aminoethyl ether)-N,N,N',N'-tetraacetic acid
50.0 micromolarIP3inositol triphosphate

Details: 150mM Nacl 50mM Tris-HCl, pH 8.0 2mM DTT 0.06% Digitonin 5mM EGTA 50 micromolar IP3
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2 seconds prior to freezing.
Detailstype 3 inositol 1,4,5-trisphosphate receptor in detergent micelles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
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: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 4519 / Average exposure time: 8.0 sec. / Average electron dose: 61.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 302966
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: CryoSPARC initial model
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN
Final 3D classificationNumber classes: 7 / Avg.num./class: 43281 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 27334
DetailsMovie frames were aligned with MotionCor2

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 217 / Target criteria: map-to-model FSC
Output model

PDB-6dr0:
Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor

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