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- EMDB-45604: cryo-EM structure of calcineurin-fused beta2 adrenergic receptor ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45604
Titlecryo-EM structure of calcineurin-fused beta2 adrenergic receptor in carazolol bound inactive state
Map data
Sample
  • Complex: calcineurin fused beta2AR in complex with FKBP12
    • Complex: calcineurin fused beta2AR
      • Protein or peptide: Beta-2 adrenergic receptor,Calcineurin subunit B type 1
    • Complex: Protein phosphatase 3 catalytic subunit alpha
      • Protein or peptide: Protein phosphatase 3 catalytic subunit alpha
    • Complex: FKBP1A
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Ligand: (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
  • Ligand: 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
KeywordsGPCR / cryo-EM / calcineurin fusion / inactive state / MEMBRANE PROTEIN / MEMBRANE PROTEIN-HYDROLASE-ISOMERASE complex
Function / homology
Function and homology information


CLEC7A (Dectin-1) induces NFAT activation / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / Calcineurin activates NFAT / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / positive regulation of saliva secretion ...CLEC7A (Dectin-1) induces NFAT activation / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / Calcineurin activates NFAT / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / calmodulin-dependent protein phosphatase activity / positive regulation of calcium ion import across plasma membrane / calcineurin complex / positive regulation of connective tissue replacement / calcineurin-mediated signaling / Ca2+ pathway / negative regulation of dendrite morphogenesis / FCERI mediated Ca+2 mobilization / protein serine/threonine phosphatase complex / slit diaphragm / macrolide binding / activin receptor binding / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transition between fast and slow fiber / regulation of synaptic vesicle cycle / transforming growth factor beta receptor binding / signaling receptor inhibitor activity / TGFBR1 LBD Mutants in Cancer / positive regulation of calcineurin-NFAT signaling cascade / type I transforming growth factor beta receptor binding / myelination in peripheral nervous system / negative regulation of activin receptor signaling pathway / heart trabecula formation / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / I-SMAD binding / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / regulation of postsynaptic neurotransmitter receptor internalization / regulation of amyloid precursor protein catabolic process / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / terminal cisterna / ryanodine receptor complex / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / negative regulation of smooth muscle contraction / positive regulation of lipophagy / ventricular cardiac muscle tissue morphogenesis / protein maturation by protein folding / 'de novo' protein folding / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine phosphatase activity / branching involved in blood vessel morphogenesis / postsynaptic modulation of chemical synaptic transmission / FK506 binding / cyclosporin A binding / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cardiac muscle hypertrophy / diet induced thermogenesis / positive regulation of activated T cell proliferation / positive regulation of protein kinase A signaling / neuronal dense core vesicle / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / positive regulation of endocytosis / phosphoprotein phosphatase activity / protein peptidyl-prolyl isomerization / adenylate cyclase binding / Calcineurin activates NFAT / regulation of immune response / DARPP-32 events / smooth muscle contraction / Activation of BAD and translocation to mitochondria / epidermis development / regulation of ryanodine-sensitive calcium-release channel activity / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / potassium channel regulator activity / bone resorption / multicellular organismal response to stress
Similarity search - Function
Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Beta 2 adrenoceptor / Adrenoceptor family / : / Calcineurin-like phosphoesterase domain, ApaH type ...Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Beta 2 adrenoceptor / Adrenoceptor family / : / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / G-protein coupled receptors family 1 signature. / EF-hand domain / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / EF-hand domain pair
Similarity search - Domain/homology
Beta-2 adrenergic receptor / Peptidyl-prolyl cis-trans isomerase FKBP1A / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJun X / Geng C / Yang D / Brian KK
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Calcineurin-fusion facilitates Cryo-EM Structure Determination of a Family A GPCR
Authors: Jun X
History
DepositionJul 2, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45604.png

Downloads & links

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Map

FileDownload / File: emd_45604.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.567482 - 4.6001105
Average (Standard dev.)0.009945005 (±0.07515255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45604_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45604_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : calcineurin fused beta2AR in complex with FKBP12

EntireName: calcineurin fused beta2AR in complex with FKBP12
Components
  • Complex: calcineurin fused beta2AR in complex with FKBP12
    • Complex: calcineurin fused beta2AR
      • Protein or peptide: Beta-2 adrenergic receptor,Calcineurin subunit B type 1
    • Complex: Protein phosphatase 3 catalytic subunit alpha
      • Protein or peptide: Protein phosphatase 3 catalytic subunit alpha
    • Complex: FKBP1A
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Ligand: (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
  • Ligand: 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN

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Supramolecule #1: calcineurin fused beta2AR in complex with FKBP12

SupramoleculeName: calcineurin fused beta2AR in complex with FKBP12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: calcineurin fused beta2AR

SupramoleculeName: calcineurin fused beta2AR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Protein phosphatase 3 catalytic subunit alpha

SupramoleculeName: Protein phosphatase 3 catalytic subunit alpha / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: FKBP1A

SupramoleculeName: FKBP1A / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2 adrenergic receptor,Calcineurin subunit B type 1

MacromoleculeName: Beta-2 adrenergic receptor,Calcineurin subunit B type 1
type: protein_or_peptide / ID: 1
Details: residues 29-354 (Uniprot numbering) of the beta2-AR with the third cytoplasmic domain replaced with residues 16-170 (Uniprot numbering) of calcineurin subunit B
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.309711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DEVWVVGMGI VMSLIVLAIV FGNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILMKM WTFGNFWCEF WTSIDVLCV TASIETLCVI AVDRYFAITS PFKYQSLLTK NKARVIILMV WIVSGLTSFL PIQMHWYRAT HQEAINCYAE E TCCDFFTN ...String:
DEVWVVGMGI VMSLIVLAIV FGNVLVITAI AKFERLQTVT NYFITSLACA DLVMGLAVVP FGAAHILMKM WTFGNFWCEF WTSIDVLCV TASIETLCVI AVDRYFAITS PFKYQSLLTK NKARVIILMV WIVSGLTSFL PIQMHWYRAT HQEAINCYAE E TCCDFFTN QAYAIASSIV SFYVPLVIMV FVYSRVFQEA KRQLDADEIK RLGKRFKKLD LDNSGSLSVE EFMSLPELQQ NP LVQRVID IFDTDGNGEV DFKEFIEGVS QFSVKGDKEQ KLRFAFRIYD MDKDGYISNG ELFQVLKMMV GNNLKDTQLQ QIV DKTIIN ADKDGDGRIS FEEFCAVVGG LDIHKKMVVD VKFCLKEHKA LKTLGIIMGT FTLCWLPFFI VNIVHVIQDN LIRK EVYIL LNWIGYVNSG FNPLIYCRSP DFRIAFQELL CLRRDDLKAY GNGY

UniProtKB: Beta-2 adrenergic receptor, Calcineurin subunit B type 1, Beta-2 adrenergic receptor

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Macromolecule #2: Protein phosphatase 3 catalytic subunit alpha

MacromoleculeName: Protein phosphatase 3 catalytic subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 42.627785 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SEPKAIDPKL STTDRVVKAV PFPPSHRLTA KEVFDNDGKP RVDILKAHLM KEGRLEESVA LRIITEGASI LRQEKNLLDI DAPVTVCGD IHGQFFDLMK LFEVGGSPAN TRYLFLGDYV DRGYFSIECV LYLWALKILY PKTLFLLRGN HECRHLTEYF T FKQECKIK ...String:
SEPKAIDPKL STTDRVVKAV PFPPSHRLTA KEVFDNDGKP RVDILKAHLM KEGRLEESVA LRIITEGASI LRQEKNLLDI DAPVTVCGD IHGQFFDLMK LFEVGGSPAN TRYLFLGDYV DRGYFSIECV LYLWALKILY PKTLFLLRGN HECRHLTEYF T FKQECKIK YSERVYDACM DAFDCLPLAA LMNQQFLCVH GGLSPEINTL DDIRKLDRFK EPPAYGPMCD ILWSDPLEDF GN EKTQEHF THNTVRGCSY FYSYPAVCDF LQHNNLLSIL RAHEAQDAGY RMYRKSQTTG FPSLITIFSA PNYLDVYNNK AAV LKYENN VMNIRQFNCS PHPYWLPNFM DVFTWSLPFV GEKVTEMLVN VLNI

UniProtKB: Protein phosphatase 3 catalytic subunit alpha

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Macromolecule #3: Peptidyl-prolyl cis-trans isomerase FKBP1A

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.967705 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGVQVETISP GDGRTFPKRG QTCVVHYTGM LEDGKKFDSS RDRNKPFKFM LGKQEVIRGW EEGVAQMSVG QRAKLTISPD YAYGATGHP GIIPPHATLV FDVELLKLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1A

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Macromolecule #4: (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol

MacromoleculeName: (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
type: ligand / ID: 4 / Number of copies: 1 / Formula: CAU
Molecular weightTheoretical: 298.379 Da
Chemical component information

ChemComp-CAU:
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol

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Macromolecule #5: 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN

MacromoleculeName: 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: FK5
Molecular weightTheoretical: 804.018 Da
Chemical component information

ChemComp-FK5:
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / medication*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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2rh1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 276093
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE

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