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- EMDB-27983: Structure of the full-length IP3R1 channel determined in the pres... -

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Entry
Database: EMDB / ID: EMD-27983
TitleStructure of the full-length IP3R1 channel determined in the presence of Calcium/IP3/ATP
Map datacryo-EM consensus map of Calcium/IP3/ATP bound IP3R1
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: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • 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
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 / inositol 1,4,5-trisphosphate-gated calcium channel activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / calcium import into the mitochondrion / voluntary musculoskeletal movement / positive regulation of hepatocyte proliferation / 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 / nuclear inner membrane / Ion homeostasis / transport vesicle membrane / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of cytosolic calcium ion concentration / single fertilization / calcium channel inhibitor activity / release of sequestered calcium ion into cytosol / liver regeneration / phosphatidylinositol binding / synaptic membrane / secretory granule membrane / cellular response to cAMP / sarcoplasmic reticulum / post-embryonic development / positive regulation of neuron projection development / positive regulation of insulin secretion / GABA-ergic synapse / Schaffer collateral - CA1 synapse / cell morphogenesis / 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 / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / 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: 3.5 Å
AuthorsFan G / Baker MR / Terry LE / Arige V / Chen M / Seryshev AB / Baker ML / Ludtke SJ / Yule DI / Serysheva II
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 General Medical Sciences (NIH/NIGMS)R01GM080139 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE019245 United States
Welch FoundationAU-2014-20190330 United States
Welch FoundationAU-2014-20220331 United States
American Heart Association18CDA34110086 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190602 United States
CitationJournal: Nat Commun / Year: 2022
Title: Conformational motions and ligand-binding underlying gating and regulation in IPR channel.
Authors: Guizhen Fan / Mariah R Baker / Lara E Terry / Vikas Arige / Muyuan Chen / Alexander B Seryshev / Matthew L Baker / Steven J Ludtke / David I Yule / Irina I Serysheva /
Abstract: Inositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single ...Inositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IPR1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP, Ca and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IPR channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
History
DepositionAug 29, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27983.png

Downloads & links

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Map

FileDownload / File: emd_27983.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM consensus map of Calcium/IP3/ATP bound IP3R1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 336 pix.
= 359.52 Å		1.07 Å/pix.
x 336 pix.
= 359.52 Å		1.07 Å/pix.
x 336 pix.
= 359.52 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: 0.011
Minimum - Maximum-0.048775006 - 0.092736535
Average (Standard dev.)0.00030213792 (±0.0030874098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 359.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: cryo-EM half map of Calcium/IP3/ATP bound IP3R1

Fileemd_27983_half_map_1.map
Annotationcryo-EM half map of Calcium/IP3/ATP bound IP3R1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map of Calcium/IP3/ATP bound IP3R1

Fileemd_27983_half_map_2.map
Annotationcryo-EM half map of Calcium/IP3/ATP bound IP3R1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
  • Ligand: CALCIUM ION
  • 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

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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: 313.657406 KDa
SequenceString: MSDKMSSFLH IGDICSLYAE GSTNGFISTL GLVDDRCVVQ PEAGDLNNPP KKFRDCLFKL CPMNRYSAQK QFWKAAKPGA NSTTDAVLL NKLHHAADLE KKQNETENRK LLGTVIQYGN VIQLLHLKSN KYLTVNKRLP ALLEKNAMRV TLDEAGNEGS W FYIQPFYK ...String:
MSDKMSSFLH IGDICSLYAE GSTNGFISTL GLVDDRCVVQ PEAGDLNNPP KKFRDCLFKL CPMNRYSAQK QFWKAAKPGA NSTTDAVLL NKLHHAADLE KKQNETENRK LLGTVIQYGN VIQLLHLKSN KYLTVNKRLP ALLEKNAMRV TLDEAGNEGS W FYIQPFYK LRSIGDSVVI GDKVVLNPVN AGQPLHASSH QLVDNPGCNE VNSVNCNTSW KIVLFMKWSD NKDDILKGGD VV RLFHAEQ EKFLTCDEHR KKQHVFLRTT GRQSATSATS SKALWEVEVV QHDPCRGGAG YWNSLFRFKH LATGHYLAAE VDP DFEEEC LEFQPSVDPD QDASRSRLRN AQEKMVYSLV SVPEGNDISS IFELDPTTLR GGDSLVPRNS YVRLRHLCTN TWVH STNIP IDKEEEKPVM LKIGTSPLKE DKEAFAIVPV SPAEVRDLDF ANDASKVLGS IAGKLEKGTI TQNERRSVTK LLEDL VYFV TGGTNSGQDV LEVVFSKPNR ERQKLMREQN ILKQIFKLLQ APFTDCGDGP MLRLEELGDQ RHAPFRHICR LCYRVL RHS QQDYRKNQEY IAKQFGFMQK QIGYDVLAED TITALLHNNR KLLEKHITAA EIDTFVSLVR KNREPRFLDY LSDLCVS MN KSIPVTQELI CKAVLNPTNA DILIETKLVL SRFEFEGVST GENALEAGED EEEVWLFWRD SNKEIRSKSV RELAQDAK E GQKEDRDVLS YYRYQLNLFA RMCLDRQYLA INEISGQLDV DLILRCMSDE NLPYDLRASF CRLMLHMHVD RDPQEQVTP VKYARLWSEI PSEIAIDDYD SSGASKDEIK ERFAQTMEFV EEYLRDVVCQ RFPFSDKEKN KLTFEVVNLA RNLIYFGFYN FSDLLRLTK ILLAILDCVH VTTIFPISKM TKGEENKGSN VMRSIHGVGE LMTQVVLRGG GFLPMTPMAA APEGNVKQAE P EKEDIMVM DTKLKIIEIL QFILNVRLDY RISCLLCIFK REFDESNSQS SETSSGNSSQ EGPSNVPGAL DFEHIEEQAE GI FGGSEEN TPLDLDDHGG RTFLRVLLHL TMHDYPPLVS GALQLLFRHF SQRQEVLQAF KQVQLLVTSQ DVDNYKQIKQ DLD QLRSIV EKSELWVYKG QGPDEPMDGA SGENEHKKTE EGTSKPLKHE STSSYNYRVV KEILIRLSKL CVQESASVRK SRKQ QQRLL RNMGAHAVVL ELLQIPYEKA EDTKMQEIMR LAHEFLQNFC AGNQQNQALL HKHINLFLNP GILEAVTMQH IFMNN FQLC SEINERVVQH FVHCIETHGR NVQYIKFLQT IVKAEGKFIK KCQDMVMAEL VNSGEDVLVF YNDRASFQTL IQMMRS ERD RMDENSPLFM YHIHLVELLA VCTEGKNVYT EIKCNSLLPL DDIVRVVTHE DCIPEVKIAY INFLNHCYVD TEVEMKE IY TSNHMWKLFE NFLVDICRAC NNTSDRKHAD SVLEKYVTEI VMSIVTTFFS SPFSDQSTTL QTRQPVFVQL LQGVFRVY H CNWLMPSQKA SVESCIRVLS DVAKSRAIAI PVDLDSQVNN LFLKSHNIVQ KTAMNWRLSA RNAARRDSVL AASRDYRNI IERLQDIVSA LEDRLRPLVQ AELSVLVDVL HRPELLFPEN TDARRKCESG GFICKLIKHT KQLLEENEEK LCIKVLQTLR EMMTKDRGY GEKQISIDEL ENAELPQPPE AENSTEQELE PSPPLRQLED HKRGEALRQI LVNRYYGNIR PSGRRESLTS F GNGPLSPG GPSKPGGGGG GPGSGSTSRG EMSLAEVQCH LDKEGASNLV IDLIMNASSD RVFHESILLA IALLEGGNTT IQ HSFFCRL TEDKKSEKFF KVFYDRMKVA QQEIKATVTV NTSDLGNKKK DDEVDRDAPS RKKAKEPTTQ ITEEVRDQLL EAS AATRKA FTTFRREADP DDHYQSGEGT QATTDKAKDD LEMSAVITIM QPILRFLQLL CENHNRDLQN FLRCQNNKTN YNLV CETLQ FLDCICGSTT GGLGLLGLYI NEKNVALINQ TLESLTEYCQ GPCHENQNCI ATHESNGIDI ITALILNDIN PLGKK RMDL VLELKNNASK LLLAIMESRH DSENAERILY NMRPKELVEV IKKAYMQGEV EFEDGENGED GAASPRNVGH NIYILA HQL ARHNKELQTM LKPGGQVDGD EALEFYAKHT AQIEIVRLDR TMEQIVFPVP SICEFLTKES KLRIYYTTER DEQGSKI ND FFLRSEDLFN EMNWQKKLRA QPVLYWCARN MSFWSSISFN LAVLMNLLVA FFYPFKGVRG GTLEPHWSGL LWTAMLIS L AIVIALPKPH GIRALIASTI LRLIFSVGLQ PTLFLLGAFN VCNKIIFLMS FVGNCGTFTR GYRAMVLDVE FLYHLLYLL ICAMGLFVHE FFYSLLLFDL VYREETLLNV IKSVTRNGRP IILTAALALI LVYLFSIVGY LFFKDDFILE VDRLPNETAG PETGESLAN DFLYSDVCRV ETGENCTSPA PKEELLPVEE TEQDKEHTCE TLLMCIVTVL SHGLRSGGGV GDVLRKPSKE E PLFAARVI YDLLFFFMVI IIVLNLIFGV IIDTFADLRS EKQKKEEILK TTCFICGLER DKFDNKTVTF EEHIKEEHNM WH YLCFIVL VKVKDSTEYT GPESYVAEMI RERNLDWFPR MRAMSLVSSD SEGEQNELRN LQEKLESTMK LVTNLSGQLS ELK DQMTEQ RKQKQRIGLL GHPPHMNVNP QQPA

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

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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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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

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

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 16 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: (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: 6 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsreconstituted in lipid nanodisc

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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 / Number real images: 24478 / Average exposure time: 0.2 sec. / Average electron dose: 49.0 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: 2.5 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

Particle selectionNumber selected: 1452797 / Details: NeuralNet autopicking in EMAN2
Startup modelType of model: EMDB MAP
EMDB ID:

23337


Details: filtered to 60 angstroms
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 133740
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

7lhe


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

PDB-8ear:
Structure of the full-length IP3R1 channel determined in the presence of Calcium/IP3/ATP

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