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- EMDB-30603: Cryo-EM structure of the cortisol-bound adhesion receptor GPR97-G... -

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Basic information

Entry
Database: EMDB / ID: EMD-30603
TitleCryo-EM structure of the cortisol-bound adhesion receptor GPR97-Go complex
Map data
Sample
  • Complex: Cortisol-bound adhesion receptor GPR97-Go complex
    • Complex: Adhesion G protein-coupled receptor G3; GPR97
      • Protein or peptide: Adhesion G protein-coupled receptor G3; GPR97
    • Complex: Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione
  • Ligand: CHOLESTEROL
  • Ligand: water
Function / homology
Function and homology information


negative regulation of CREB transcription factor activity / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / negative regulation of non-canonical NF-kappaB signal transduction / dopamine receptor signaling pathway / G protein-coupled serotonin receptor binding / specific granule membrane / regulation of cell migration / B cell differentiation / muscle contraction ...negative regulation of CREB transcription factor activity / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / negative regulation of non-canonical NF-kappaB signal transduction / dopamine receptor signaling pathway / G protein-coupled serotonin receptor binding / specific granule membrane / regulation of cell migration / B cell differentiation / muscle contraction / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. ...GPCR, family 2, orphan receptor, GPR1/GPR3/GPR5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(o) subunit alpha / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Adhesion G protein-coupled receptor G3
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPing Y / Mao C / Xiao P / Zhao R / Jiang Y / Yang Z / An W / Shen D / Yang F / Zhang H ...Ping Y / Mao C / Xiao P / Zhao R / Jiang Y / Yang Z / An W / Shen D / Yang F / Zhang H / Qu C / Shen Q / Tian C / Li Z / Li S / Wang G / Tao X / Wen X / Zhong Y / Yang J / Yi F / Yu X / Xu E / Zhang Y / Sun J
CitationJournal: Nature / Year: 2021
Title: Structures of the glucocorticoid-bound adhesion receptor GPR97-G complex.
Authors: Yu-Qi Ping / Chunyou Mao / Peng Xiao / Ru-Jia Zhao / Yi Jiang / Zhao Yang / Wen-Tao An / Dan-Dan Shen / Fan Yang / Huibing Zhang / Changxiu Qu / Qingya Shen / Caiping Tian / Zi-Jian Li / ...Authors: Yu-Qi Ping / Chunyou Mao / Peng Xiao / Ru-Jia Zhao / Yi Jiang / Zhao Yang / Wen-Tao An / Dan-Dan Shen / Fan Yang / Huibing Zhang / Changxiu Qu / Qingya Shen / Caiping Tian / Zi-Jian Li / Shaolong Li / Guang-Yu Wang / Xiaona Tao / Xin Wen / Ya-Ni Zhong / Jing Yang / Fan Yi / Xiao Yu / H Eric Xu / Yan Zhang / Jin-Peng Sun /
Abstract: Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available. Here we report that glucocorticoid stress ...Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available. Here we report that glucocorticoid stress hormones activate adhesion G-protein-coupled receptor G3 (ADGRG3; also known as GPR97), a prototypical adhesion GPCR. The cryo-electron microscopy structures of GPR97-G complexes bound to the anti-inflammatory drug beclomethasone or the steroid hormone cortisol revealed that glucocorticoids bind to a pocket within the transmembrane domain. The steroidal core of glucocorticoids is packed against the 'toggle switch' residue W, which senses the binding of a ligand and induces activation of the receptor. Active GPR97 uses a quaternary core and HLY motif to fasten the seven-transmembrane bundle and to mediate G protein coupling. The cytoplasmic side of GPR97 has an open cavity, where all three intracellular loops interact with the G protein, contributing to the high basal activity of GRP97. Palmitoylation at the cytosolic tail of the G protein was found to be essential for efficient engagement with GPR97 but is not observed in other solved GPCR complex structures. Our work provides a structural basis for ligand binding to the seven-transmembrane domain of an adhesion GPCR and subsequent G protein coupling.
History
DepositionOct 3, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-7d77
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30603.png

Downloads & links

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Map

FileDownload / File: emd_30603.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.3748775 - 0.5125429
Average (Standard dev.)-0.00014808896 (±0.013773715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 194.68802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z194.688194.688194.688
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.3750.513-0.000

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Supplemental data

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Sample components

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Entire : Cortisol-bound adhesion receptor GPR97-Go complex

EntireName: Cortisol-bound adhesion receptor GPR97-Go complex
Components
  • Complex: Cortisol-bound adhesion receptor GPR97-Go complex
    • Complex: Adhesion G protein-coupled receptor G3; GPR97
      • Protein or peptide: Adhesion G protein-coupled receptor G3; GPR97
    • Complex: Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: Cortisol-bound adhesion receptor GPR97-Go complex

SupramoleculeName: Cortisol-bound adhesion receptor GPR97-Go complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Adhesion G protein-coupled receptor G3; GPR97

SupramoleculeName: Adhesion G protein-coupled receptor G3; GPR97 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: sf9

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Supramolecule #3: Go

SupramoleculeName: Go / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: sf9

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Supramolecule #4: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: sf9

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Macromolecule #1: Guanine nucleotide-binding protein G(o) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.286922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT ...String:
MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT YEDAAAYIQA QFESKNRSPN KEIYCHMTCA TDTNNAQVIF DAVTDIIIAN NLRGCGLY

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.245801 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWNHHHHHH

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #4: Adhesion G protein-coupled receptor G3; GPR97

MacromoleculeName: Adhesion G protein-coupled receptor G3; GPR97 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.767098 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTQEKPTEGP RNTCLGSNNM YDIFNLNDKA LCFTKCRQSG SDSCNVENLQ RYWLNYEAH LMKEGLTQKV NTPFLKALVQ NLSTNTAEDF YFSLEPSQVP RQVMKDEDKP PDRVRLPKSL FRSLPGNRSV V RLAVTILD ...String:
DYKDDDDAKL QTMHHHHHHH HHHENLYFQG GTQEKPTEGP RNTCLGSNNM YDIFNLNDKA LCFTKCRQSG SDSCNVENLQ RYWLNYEAH LMKEGLTQKV NTPFLKALVQ NLSTNTAEDF YFSLEPSQVP RQVMKDEDKP PDRVRLPKSL FRSLPGNRSV V RLAVTILD IGPGTLFKGP RLGLGDGSGV LNNRLVGLSV GQMHVTKLAE PLEIVFSHQR PPPNMTLTCV FWDVTKGTTG DW SSEGCST EVRPEGTVCC CDALAFFALL LRPTLDQSTV HILTRISQAG CGVSMIFLAF TIILYAFLRL SRERFKSEDA PKI HVALGG SLFLLNLAFL VNVGSGSKGS DAACWARGAV FHYFLLCAFT WMGLEAFHLY LLAVRVFNTY FGHYFLKLSL VGWG LPALM VIGTGSANSY GLYTIRDREN RTSLELCWFR EGTTMYALYI TVHGYFLITF LFGMVVLALV VWKIFTLSRA TAVKE RGKN RKKVLTLLGL SSLVGVTWGL AIFTPLGLST VYIFALFNSL QGVFICCWFT ILYLPSQSTT VSSSTARLDQ AHSASQ E

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Macromolecule #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.610615 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGS

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #8: (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione

MacromoleculeName: (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione
type: ligand / ID: 8 / Number of copies: 1 / Formula: HCY
Molecular weightTheoretical: 362.46 Da
Chemical component information

ChemComp-HCY:
(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / medication, hormone*YM / Cortisol

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Macromolecule #9: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 1 / 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: 7.5
GridModel: Quantifoil / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49310 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 5871 / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4323518
CTF correctionSoftware - Name: Gctf (ver. v1.18)
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta2) / Number images used: 75814
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6g79

Output model

PDB-7d77:
Cryo-EM structure of the cortisol-bound adhesion receptor GPR97-Go complex

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