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- EMDB-41350: Human Type 3 IP3 Receptor - Resting State (+IP3/ATP) -

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Basic information

Entry
Database: EMDB / ID: EMD-41350
TitleHuman Type 3 IP3 Receptor - Resting State (+IP3/ATP)
Map dataIP3 Receptor - hIP3R3 Inhibited State - Tetramer Composite (Chimera 'vop maximum' of four aligned density modified single protomer composite maps)
Sample
  • Complex: Human Type 3 IP3 Receptor
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 3
  • Ligand: ZINC ION
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
KeywordsIon Channel / Calcium Channel / Endoplasmic Reticulum / TRANSPORT PROTEIN
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: 2.5 Å
AuthorsPaknejad N / Sapuru V / Hite RK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM13230704 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA008748 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243235 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural titration reveals Ca-dependent conformational landscape of the IP receptor.
Authors: Navid Paknejad / Vinay Sapuru / Richard K Hite /
Abstract: Inositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division ...Inositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IPR-mediated Ca responses, the structural underpinnings of the biphasic Ca dependence that underlies Ca oscillations are incompletely understood. Here, we collect cryo-EM images of an IPR with Ca concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca binding at a high-affinity site allows IPRs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca concentrations, IPRs preferentially enter an inhibited state stabilized by a second, low-affinity Ca binding site. Together, these studies provide a mechanistic basis for the biphasic Ca-dependence of IPR channel activity.
History
DepositionJul 25, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41350.png

Downloads & links

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Map

FileDownload / File: emd_41350.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Tetramer Composite (Chimera 'vop maximum' of four aligned density modified single protomer composite maps)
Voxel sizeX=Y=Z: 0.629 Å
Density
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-57.161453000000002 - 113.115920000000003
Average (Standard dev.)0.14564125 (±1.9009858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 422.68802 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - ARM2...

Fileemd_41350_additional_1.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - ARM2 Local Refinement (1 Chain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - Consensus...

Fileemd_41350_additional_10.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Consensus Refinement - Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - Cytosolic...

Fileemd_41350_additional_2.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Cytosolic Domain (CD) Local Refinement (1 Chain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - Single...

Fileemd_41350_additional_3.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Single Protomer Local Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - CLD/ARM3...

Fileemd_41350_additional_4.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - CLD/ARM3 Local Refinement (1 Chain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - Consensus Refinement

Fileemd_41350_additional_5.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Consensus Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - JD/TMD...

Fileemd_41350_additional_6.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - JD/TMD Local Refinement (1 Chain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - BTF1/BTF2/ARM1...

Fileemd_41350_additional_7.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - BTF1/BTF2/ARM1 Local Refinement (1 Chain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - 1...

Fileemd_41350_additional_8.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - 1 Chain Composite (Phenix Resolve_CryoEM for each local refinement, Phenix Combine_Focused_Maps using final model)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IP3 Receptor - hIP3R3 Inhibited State - Consensus...

Fileemd_41350_additional_9.map
AnnotationIP3 Receptor - hIP3R3 Inhibited State - Consensus Refinement - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Type 3 IP3 Receptor

EntireName: Human Type 3 IP3 Receptor
Components
  • Complex: Human Type 3 IP3 Receptor
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 3
  • Ligand: ZINC ION
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Human Type 3 IP3 Receptor

SupramoleculeName: Human Type 3 IP3 Receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: In the presence of saturating IP3, ATP, and Ca2+ titrated from 1 nM to 10 um
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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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

UniProtKB: Inositol 1,4,5-trisphosphate receptor type 3

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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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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #6: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 24 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 640 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration20 mg/mL
BufferpH: 8
Details: 120 mM NaCl, 50 mM Tris-HCl pH 8.0, 0.02% LMNG, 2 mM dithiothreitol, 2 mM EDTA, 2 mM EGTA, 2 mM BAPTA, 2 mM HEDTA, 1 mM ATP, 500 uM fluorinated fos-choline-8, 3 mM free Mg2+, 1-10000 nM free Ca2+
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Custom-made calcium free blotting paper (see publication for details)..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.3 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6 / Number real images: 17733 / Average exposure time: 3.0 sec. / Average electron dose: 66.0 e/Å2
Details: Images were collected at 0.826 A/px magnification on an FEI Krios with Gatan K3 detector at 15 e-/pix/sec with 3 sec exposure (0.05 sec/frame) for a total dose of 66 e-/A2 in automated ...Details: Images were collected at 0.826 A/px magnification on an FEI Krios with Gatan K3 detector at 15 e-/pix/sec with 3 sec exposure (0.05 sec/frame) for a total dose of 66 e-/A2 in automated fashion using SerialEM. Five datasets were collected during the same session for each Ca2+ concentration on a series of grids that were prepared sequentially resulting in 637 movies at 1 nM, 2150 movies at 10 nM, 6126 movies at 100 nM, 1372 movies at 1 uM, and 3136 movies at 10 uM. A sixth dataset of 4312 movies collected at nominal 100 nM free Ca2+ from a grid prepared later in the sequence was collected as a technical replicate to assess experimental error.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 3668312

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Target criteria: Map to Model FSC
Output model

PDB-8tkg:
Human Type 3 IP3 Receptor - Resting State (+IP3/ATP)

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