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- EMDB-23337: Structure of full-length IP3R1 channel reconstituted into lipid n... -

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Basic information

Entry
Database: EMDB / ID: EMD-23337
TitleStructure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state
Map dataCryo-EM structure of full-length IP3R1 in nanodisc (apo-state)
Sample
  • Complex: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 1
  • Ligand: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
  • Ligand: ZINC ION
KeywordsCalcium channel / lipid nanodisc / MEMBRANE PROTEIN
Function / homology
Function and homology information


Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / smooth endoplasmic reticulum membrane / cGMP effects / Elevation of cytosolic Ca2+ levels / platelet dense tubular network / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / smooth endoplasmic reticulum membrane / cGMP effects / Elevation of cytosolic Ca2+ levels / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / : / epithelial fluid transport / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / calcium import into the mitochondrion / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / negative regulation of calcium-mediated signaling / positive regulation of calcium ion transport / endoplasmic reticulum calcium ion homeostasis / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of hepatocyte proliferation / nuclear inner membrane / Ion homeostasis / transport vesicle membrane / ligand-gated ion channel signaling pathway / dendrite development / intracellularly gated calcium channel activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / single fertilization / regulation of cytosolic calcium ion concentration / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / phosphatidylinositol binding / secretory granule membrane / liver regeneration / sarcoplasmic reticulum / post-embryonic development / GABA-ergic synapse / synaptic membrane / Schaffer collateral - CA1 synapse / cell morphogenesis / positive regulation of insulin secretion / positive regulation of neuron projection development / calcium ion transport / nuclear envelope / presynapse / positive regulation of cytosolic calcium ion concentration / protein phosphatase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / protein homotetramerization / cellular response to hypoxia / transmembrane transporter binding / response to hypoxia / postsynapse / postsynaptic density / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / 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 / Armadillo-type fold
Similarity search - Domain/homology
Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBaker MR / Fan G
Funding support United States, 7 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 Neurological Disorders and Stroke (NIH/NINDS)R21NS106968 United States
Welch FoundationAU-2014-20190330 United States
American Heart Association18CDA34110086 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM063210 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY025218 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY026545 United States
CitationJournal: Commun Biol / Year: 2021
Title: Cryo-EM structure of type 1 IPR channel in a lipid bilayer.
Authors: Mariah R Baker / Guizhen Fan / Alexander B Seryshev / Melina A Agosto / Matthew L Baker / Irina I Serysheva /
Abstract: Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved ...Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IPR1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IPR1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IPR1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating.
History
DepositionJan 22, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.263
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.263
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lhe
  • Surface level: 0.263
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23337.png

Downloads & links

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Map

FileDownload / File: emd_23337.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of full-length IP3R1 in nanodisc (apo-state)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 440 pix.
= 470.8 Å		1.07 Å/pix.
x 440 pix.
= 470.8 Å		1.07 Å/pix.
x 440 pix.
= 470.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.263 / Movie #1: 0.263
Minimum - Maximum-0.70018005 - 1.7539629
Average (Standard dev.)0.0042232326 (±0.039588977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 470.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z470.800470.800470.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.7001.7540.004

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Supplemental data

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Sample components

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Entire : Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein c...

EntireName: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex
Components
  • Complex: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex
    • Protein or peptide: Inositol 1,4,5-trisphosphate receptor type 1
  • Ligand: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
  • Ligand: ZINC ION

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Supramolecule #1: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein c...

SupramoleculeName: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: 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 type 1

MacromoleculeName: Inositol 1,4,5-trisphosphate receptor type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: cerebellum
Molecular weightTheoretical: 311.84825 KDa
SequenceString: SSFLHIGDIC SLYAEGSTNG FISTLGLVDD RCVVQPEAGD LNNPPKKFRD CLFKLCPMNR YSAQKQFWKA AKPGANSTTD AVLLNKLHH AADLEKKQNE TENRKLLGTV IQYGNVIQLL HLKSNKYLTV NKRLPALLEK NAMRVTLDEA GNEGSWFYIQ P FYKLRSIG ...String:
SSFLHIGDIC SLYAEGSTNG FISTLGLVDD RCVVQPEAGD LNNPPKKFRD CLFKLCPMNR YSAQKQFWKA AKPGANSTTD AVLLNKLHH AADLEKKQNE TENRKLLGTV IQYGNVIQLL HLKSNKYLTV NKRLPALLEK NAMRVTLDEA GNEGSWFYIQ P FYKLRSIG DSVVIGDKVV LNPVNAGQPL HASSHQLVDN PGCNEVNSVN CNTSWKIVLF MKWSDNKDDI LKGGDVVRLF HA EQEKFLT CDEHRKKQHV FLRTTGRQSA TSATSSKALW EVEVVQHDPC RGGAGYWNSL FRFKHLATGH YLAAEVDPDF EEE CLEFQP SVDPDQDASR SRLRNAQEKM VYSLVSVPEG NDISSIFELD PTTLRGGDSL VPRNSYVRLR HLCTNTWVHS TNIP IDKEE EKPVMLKIGT SPLKEDKEAF AIVPVSPAEV RDLDFANDAS KVLGSIAGKL EKGTITQNER RSVTKLLEDL VYFVT GGTN SGQDVLEVVF SKPNRERQKL MREQNILKQI FKLLQAPFTD CGDGPMLRLE ELGDQRHAPF RHICRLCYRV LRHSQQ DYR KNQEYIAKQF GFMQKQIGYD VLAEDTITAL LHNNRKLLEK HITAAEIDTF VSLVRKNREP RFLDYLSDLC VSMNKSI PV TQELICKAVL NPTNADILIE TKLVLSRFEF EGVSTGENAL EAGEDEEEVW LFWRDSNKEI RSKSVRELAQ DAKEGQKE D RDVLSYYRYQ LNLFARMCLD RQYLAINEIS GQLDVDLILR CMSDENLPYD LRASFCRLML HMHVDRDPQE QVTPVKYAR LWSEIPSEIA IDDYDSSGAS KDEIKERFAQ TMEFVEEYLR DVVCQRFPFS DKEKNKLTFE VVNLARNLIY FGFYNFSDLL RLTKILLAI LDCVHVTTIF PISKMTKGEE NKGSNVMRSI HGVGELMTQV VLRGGGFLPM TPMAAAPEGN VKQAEPEKED I MVMDTKLK IIEILQFILN VRLDYRISCL LCIFKREFDE SNSQSSETSS GNSSQEGPSN VPGALDFEHI EEQAEGIFGG SE ENTPLDL DDHGGRTFLR VLLHLTMHDY PPLVSGALQL LFRHFSQRQE VLQAFKQVQL LVTSQDVDNY KQIKQDLDQL RSI VEKSEL WVYKGQGPDE PMDGASGENE HKKTEEGTSK PLKHESTSSY NYRVVKEILI RLSKLCVQES ASVRKSRKQQ QRLL RNMGA HAVVLELLQI PYEKAEDTKM QEIMRLAHEF LQNFCAGNQQ NQALLHKHIN LFLNPGILEA VTMQHIFMNN FQLCS EINE RVVQHFVHCI ETHGRNVQYI KFLQTIVKAE GKFIKKCQDM VMAELVNSGE DVLVFYNDRA SFQTLIQMMR SERDRM DEN SPLFMYHIHL VELLAVCTEG KNVYTEIKCN SLLPLDDIVR VVTHEDCIPE VKIAYINFLN HCYVDTEVEM KEIYTSN HM WKLFENFLVD ICRACNNTSD RKHADSVLEK YVTEIVMSIV TTFFSSPFSD QSTTLQTRQP VFVQLLQGVF RVYHCNWL M PSQKASVESC IRVLSDVAKS RAIAIPVDLD SQVNNLFLKS HNIVQKTAMN WRLSARNAAR RDSVLAASRD YRNIIERLQ DIVSALEDRL RPLVQAELSV LVDVLHRPEL LFPENTDARR KCESGGFICK LIKHTKQLLE ENEEKLCIKV LQTLREMMTK DRGYGEKQI SIDELENAEL PQPPEAENST EQELEPSPPL RQLEDHKRGE ALRQILVNRY YGNIRPSGRR ESLTSFGNGP L SPGGPSKP GGGGGGPGSG STSRGEMSLA EVQCHLDKEG ASNLVIDLIM NASSDRVFHE SILLAIALLE GGNTTIQHSF FC RLTEDKK SEKFFKVFYD RMKVAQQEIK ATVTVNTSDL GNKKKDDEVD RDAPSRKKAK EPTTQITEEV RDQLLEASAA TRK AFTTFR READPDDHYQ SGEGTQATTD KAKDDLEMSA VITIMQPILR FLQLLCENHN RDLQNFLRCQ NNKTNYNLVC ETLQ FLDCI CGSTTGGLGL LGLYINEKNV ALINQTLESL TEYCQGPCHE NQNCIATHES NGIDIITALI LNDINPLGKK RMDLV LELK NNASKLLLAI MESRHDSENA ERILYNMRPK ELVEVIKKAY MQGEVEFEDG ENGEDGAASP RNVGHNIYIL AHQLAR HNK ELQTMLKPGG QVDGDEALEF YAKHTAQIEI VRLDRTMEQI VFPVPSICEF LTKESKLRIY YTTERDEQGS KINDFFL RS EDLFNEMNWQ KKLRAQPVLY WCARNMSFWS SISFNLAVLM NLLVAFFYPF KGVRGGTLEP HWSGLLWTAM LISLAIVI A LPKPHGIRAL IASTILRLIF SVGLQPTLFL LGAFNVCNKI IFLMSFVGNC GTFTRGYRAM VLDVEFLYHL LYLLICAMG LFVHEFFYSL LLFDLVYREE TLLNVIKSVT RNGRPIILTA ALALILVYLF SIVGYLFFKD DFILEVDRLP NETAGPETGE SLANDFLYS DVCRVETGEN CTSPAPKEEL LPVEETEQDK EHTCETLLMC IVTVLSHGLR SGGGVGDVLR KPSKEEPLFA A RVIYDLLF FFMVIIIVLN LIFGVIIDTF ADLRSEKQKK EEILKTTCFI CGLERDKFDN KTVTFEEHIK EEHNMWHYLC FI VLVKVKD STEYTGPESY VAEMIRERNL DWFPRMRAMS LVSSDSEGEQ NELRNLQEKL ESTMKLVTNL SGQLSELKDQ MTE QRKQKQ RIGLLGHP

UniProtKB: Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1

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Macromolecule #2: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...

MacromoleculeName: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
type: ligand / ID: 2 / Number of copies: 28 / Formula: PLX
Molecular weightTheoretical: 767.132 Da
Chemical component information

ChemComp-PLX:
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL / phospholipid*YM

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Digitization - Frames/image: 2-35 / Number real images: 22000 / Average exposure time: 0.2 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46943 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9248


Details: filtered to 60 angstroms
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 573723
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6mu2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7lhe:
Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state

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