[English] 日本語
Yorodumi
- EMDB-41341: Human Type 3 IP3 Receptor - Activated CTD Frame 1 (Figure S18B) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41341
TitleHuman Type 3 IP3 Receptor - Activated CTD Frame 1 (Figure S18B)
Map dataIP3 Receptor - hIP3R3 Activated CTD Frame 1 (Figure S18B) - Consensus Refinement
Sample
  • Complex: Human Type 3 IP3 Receptor
    • Protein or peptide: Human Type 3 IP3 Receptor
KeywordsIon Channel / Calcium Channel / Endoplasmic Reticulum / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory perception of bitter taste / sensory perception of umami taste / DAG and IP3 signaling / 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 / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / PLC beta mediated events ...sensory perception of bitter taste / sensory perception of umami taste / DAG and IP3 signaling / 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 / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / PLC beta mediated events / inositol hexakisphosphate binding / inositol 1,4,5 trisphosphate binding / nuclear outer membrane / CLEC7A (Dectin-1) induces NFAT activation / transport vesicle membrane / cytoplasmic side of endoplasmic reticulum membrane / brush border / intracellularly gated calcium channel activity / Role of phospholipids in phagocytosis / calcium ion homeostasis / Ion homeostasis / release of sequestered calcium ion into cytosol / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / phosphatidylinositol binding / secretory granule membrane / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sarcoplasmic reticulum / Regulation of insulin secretion / long-term synaptic potentiation / memory / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to calcium ion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / sensory perception of taste / apical part of cell / myelin sheath / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / 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-gated calcium channel ITPR3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.25 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

-
Structure visualization

Supplemental images

emd_41341.png

Downloads & links

-
Map

FileDownload / File: emd_41341.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIP3 Receptor - hIP3R3 Activated CTD Frame 1 (Figure S18B) - Consensus Refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.28442714 - 0.7926429
Average (Standard dev.)-0.0009062605 (±0.02445716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: IP3 Receptor - hIP3R3 Activated CTD Frame 1...

Fileemd_41341_half_map_1.map
AnnotationIP3 Receptor - hIP3R3 Activated CTD Frame 1 (Figure S18B) - Consensus Refinement - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: IP3 Receptor - hIP3R3 Activated CTD Frame 1...

Fileemd_41341_half_map_2.map
AnnotationIP3 Receptor - hIP3R3 Activated CTD Frame 1 (Figure S18B) - Consensus Refinement - Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Type 3 IP3 Receptor

EntireName: Human Type 3 IP3 Receptor
Components
  • Complex: Human Type 3 IP3 Receptor
    • Protein or peptide: Human Type 3 IP3 Receptor

-
Supramolecule #1: Human Type 3 IP3 Receptor

SupramoleculeName: Human Type 3 IP3 Receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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

-
Macromolecule #1: Human Type 3 IP3 Receptor

MacromoleculeName: Human Type 3 IP3 Receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSEMSSFLHI GDIVSLYAEG SVNGFISTLG LVDDRCVVEP AAGDLDNPPK KFRDCLFKVC PMNRYSAQKQ YWKAKQTKQD KEKIADVVLL QKLQHAAQME QKQNDTENKK VHGDVVKYGS VIQLLHMKSN KYLTVNKRLP ALLEKNAMRV TLDATGNEGS WLFIQPFWKL ...String:
MSEMSSFLHI GDIVSLYAEG SVNGFISTLG LVDDRCVVEP AAGDLDNPPK KFRDCLFKVC PMNRYSAQKQ YWKAKQTKQD KEKIADVVLL QKLQHAAQME QKQNDTENKK VHGDVVKYGS VIQLLHMKSN KYLTVNKRLP ALLEKNAMRV TLDATGNEGS WLFIQPFWKL RSNGDNVVVG DKVILNPVNA GQPLHASNYE LSDNAGCKEV NSVNCNTSWK INLFMQFRDH LEEVLKGGDV VRLFHAEQEK FLTCDEYKGK LQVFLRTTLR QSATSATSSN ALWEVEVVHH DPCRGGAGHW NGLYRFKHLA TGNYLAAEEN PSYKGDASDP KAAGMGAQGR TGRRNAGEKI KYCLVAVPHG NDIASLFELD PTTLQKTDSF VPRNSYVRLR HLCTNTWIQS TNVPIDIEEE RPIRLMLGTC PTKEDKEAFA IVSVPVSEIR DLDFANDASS MLASAVEKLN EGFISQNDRR FVIQLLEDLV FFVSDVPNNG QNVLDIMVTK PNRERQKLMR EQNILKQVFG ILKAPFREKG GEGPLVRLEE LSDQKNAPYQ HMFRLCYRVL RHSQEDYRKN QEHIAKQFGM MQSQIGYDIL AEDTITALLH NNRKLLEKHI TKTEVETFVS LVRKNREPRF LDYLSDLCVS NHIAIPVTQE LICKCVLDPK NSDILIRTEL RPVKEMAQSH EYLSIEYSEE EVWLTWTDKN NEHHEKSVRQ LAQEARAGNA HDENVLSYYR YQLKLFARMC LDRQYLAIDE ISQQLGVDLI FLCMADEMLP FDLRASFCHL MLHVHVDRDP QELVTPVKFA RLWTEIPTAI TIKDYDSNLN ASRDDKKNKF ANTMEFVEDY LNNVVSEAVP FANEEKNKLT FEVVSLAHNL IYFGFYSFSE LLRLTRTLLG IIDCVQGPPA MLQAYEDPGG KNVRRSIQGV GHMMSTMVLS RKQSVFSAPS LSAGASAAEP LDRSKFEENE DIVVMETKLK ILEILQFILN VRLDYRISYL LSVFKKEFVE VFPMQDSGAD GTAPAFDSTT ANMNLDRIGE QAEAMFGVGK TSSMLEVDDE GGRMFLRVLI HLTMHDYAPL VSGALQLLFK HFSQRQEAMH TFKQVQLLIS AQDVENYKVI KSELDRLRTM VEKSELWVDK KGSGKGEEVE AGAAKDKKER PTDEEGFLHP PGEKSSENYQ IVKGILERLN KMCGVGEQMR KKQQRLLKNM DAHKVMLDLL QIPYDKGDAK MMEILRYTHQ FLQKFCAGNP GNQALLHKHL HLFLTPGLLE AETMQHIFLN NYQLCSEISE PVLQHFVHLL ATHGRHVQYL DFLHTVIKAE GKYVKKCQDM IMTELTNAGD DVVVFYNDKA SLAHLLDMMK AARDGVEDHS PLMYHISLVD LLAACAEGKN VYTEIKCTSL LPLEDVVSVV THEDCITEVK MAYVNFVNHC YVDTEVEMKE IYTSNHIWTL FENFTLDMAR VCSKREKRVA DPTLEKYVLS VVLDTINAFF SSPFSENSTS LQTHQTIVVQ LLQSTTRLLE CPWLQQQHKG SVEACIRTLA MVAKGRAILL PMDLDAHISS MLSSGASCAA AAQRNASSYK ATTRAFPRVT PTANQWDYKN IIEKLQDIIT ALEERLKPLV QAELSVLVDV LHWPELLFLE GSEAYQRCES GGFLSKLIQH TKDLMESEEK LCIKVLRTLQ QMLLKKTKYG DRGNQLRKML LQNYLQNRKS TSRGDLPDPI GTGLDPDWSA IAATQCRLDK EGATKLVCDL ITSTKNEKIF QESIGLAIHL LDGGNTEIQK SFHNLMMSDK KSERFFKVLH DRMKRAQQET KSTVAVNMND LGSQPHEDRE PVDPTTKGRV ASFSIPGSSS RYSLGPSLRR GHEVSERVQS SEMGTSVLIM QPILRFLQLL CENHNRDLQN FLRCQNNKTN YNLVCETLQF LDIMCGSTTG GLGLLGLYIN EDNVGLVIQT LETLTEYCQG PCHENQTCIV THESNGIDII TALILNDISP LCKYRMDLVL QLKDNASKLL LALMESRHDS ENAERILISL RPQELVDVIK KAYLQEEERE NSEVSPREVG HNIYILALQL SRHNKQLQHL LKPVKRIQEE EAEGISSMLS LNNKQLSQML KSSAPAQEEE EDPLAYYENH TSQIEIVRQD RSMEQIVFPV PGICQFLTEE TKHRLFTTTE QDEQGSKVSD FFDQSSFLHN EMEWQRKLRS MPLIYWFSRR MTLWGSISFN LAVFINIIIA FFYPYMEGAS TGVLDSPLIS LLFWILICFS IAALFTKRYS IRPLIVALIL RSIYYLGIGP TLNILGALNL TNKIVFVVSF VGNRGTFIRG YKAMVMDMEF LYHVGYILTS VLGLFAHELF YSILLFDLIY REETLFNVIK SVTRNGRSIL LTALLALILV YLFSIVGFLF LKDDFILEVD RLPNNHSTAS PLGMPHGAAA FVDTCSGDKM DCVSGLSVPE VLEEDRELDS TERACDTLLM CIVTVMNHGL RNGGGVGDIL RKPSKDESLF PARVVYDLLF FFIVIIIVLN LIFGVIIDTF ADLRSEKQKK EEILKTTCFI CGLERDKFDN KTVSFEEHIK LEHNMWNYLY FIVLVRVKNK TDYTGPESYV AQMIKNKNLD WFPRMRAMSL VSNEGEGEQN EIRILQDKLN STMKLVSHLT AQLNELKEQM TEQRKRRQRL GFVDVQNCIS R

UniProtKB: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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)..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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.
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 FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 68453
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more