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- EMDB-63196: DOI-NBOMe-bound Serotonin 2A (5-HT2A) receptor-Gq complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63196
TitleDOI-NBOMe-bound Serotonin 2A (5-HT2A) receptor-Gq complex
Map data
Sample
  • Complex: 5-HT2AR-bound DOI in complex with Gi heterotrimer
    • 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
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha
    • Protein or peptide: 5-hydroxytryptamine receptor 2A
  • Ligand: CHOLESTEROL
  • Ligand: (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)-~{N}-[(2-methoxyphenyl)methyl]propan-2-amine
Keywordscomplex / agonist / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / neurofilament / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion ...protein localization to cytoskeleton / positive regulation of heat generation / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / neurofilament / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / sensory perception of itch / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / cell body fiber / artery smooth muscle contraction / PLC beta mediated events / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of cytokine production involved in immune response / serotonin receptor activity / regulation of platelet activation / Serotonin receptors / entrainment of circadian clock / G protein-coupled serotonin receptor activity / serotonin receptor signaling pathway / sensitization / neurotransmitter receptor activity / urinary bladder smooth muscle contraction / serotonin binding / positive regulation of platelet aggregation / regulation of canonical Wnt signaling pathway / negative regulation of synaptic transmission, glutamatergic / positive regulation of DNA biosynthetic process / glutamate receptor signaling pathway / mast cell degranulation / temperature homeostasis / detection of temperature stimulus involved in sensory perception of pain / regulation of dopamine secretion / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / negative regulation of potassium ion transport / protein tyrosine kinase activator activity / regulation of skeletal muscle contraction / phototransduction, visible light / PKA activation in glucagon signalling / positive regulation of vasoconstriction / hair follicle placode formation / developmental growth / intracellular transport / positive regulation of execution phase of apoptosis / photoreceptor outer segment / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / D1 dopamine receptor binding / postsynaptic cytosol / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / activation of adenylate cyclase activity / cellular response to acidic pH / adenylate cyclase-activating adrenergic receptor signaling pathway / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / behavioral response to cocaine / positive regulation of relaxation of smooth muscle / release of sequestered calcium ion into cytosol / Adenylate cyclase inhibitory pathway / hormone-mediated signaling pathway / D2 dopamine receptor binding / cellular response to glucagon stimulus / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / intracellular glucose homeostasis / presynaptic modulation of chemical synaptic transmission / cellular response to forskolin / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of glycolytic process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / adenylate cyclase activator activity / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / trans-Golgi network membrane / dendritic shaft / GTPase activator activity / glycolytic process / Regulation of insulin secretion / neuropeptide signaling pathway / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / bone development / G protein-coupled receptor binding / caveola / platelet aggregation / response to peptide hormone / cognition / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite
Similarity search - Function
5-Hydroxytryptamine 2A receptor / G-protein alpha subunit, group Q / 5-hydroxytryptamine receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit ...5-Hydroxytryptamine 2A receptor / G-protein alpha subunit, group Q / 5-hydroxytryptamine receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5-hydroxytryptamine receptor 2A / Guanine nucleotide-binding protein G(q) 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 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsXu Z / Shao ZH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82404716 China
CitationJournal: Nature / Year: 2026
Title: Psychedelics elicit their effects by 5-HT receptor-mediated G signalling.
Authors: Zheng Xu / Hongshuang Wang / Jingjing Yu / Yue Deng / Xiaowen Tian / Rongjun Ni / Fan Xia / Lingyi Yang / Chanjuan Xu / Liting Zhang / Renxuan Luo / Peipei Chen / Xiaoyu Zhang / Yuxuan Liu / ...Authors: Zheng Xu / Hongshuang Wang / Jingjing Yu / Yue Deng / Xiaowen Tian / Rongjun Ni / Fan Xia / Lingyi Yang / Chanjuan Xu / Liting Zhang / Renxuan Luo / Peipei Chen / Xiaoyu Zhang / Yuxuan Liu / Jingyu Hou / Miyuan Zhang / Shasha Chen / Lantian Su / Hui Sun / Yixiao He / Dandan Chen / Xiaoting Chen / Zhuang Miao / Jie Xie / Xinlei Liu / Jie Zhao / Bowen Ke / Xiaohe Tian / Linan Zeng / Lingli Zhang / Xiangdong Tang / Shengyong Yang / Jianfeng Liu / Xiaohui Wang / Wei Yan / Zhenhua Shao /
Abstract: Psychedelics are undergoing a renaissance as potential therapy for psychiatric disorders, with more than 200 clinical trials being studied across several countries. However, the precise mechanisms by ...Psychedelics are undergoing a renaissance as potential therapy for psychiatric disorders, with more than 200 clinical trials being studied across several countries. However, the precise mechanisms by which these drugs bring about benefits and the potential clinical risks are not yet fully understood. The serotonin 2A receptor (5-HTR) was reported to be a G-coupled receptor and the primary interoceptive target of psychedelics. Here we compared psychedelics and their non-hallucinogenic analogues (nHAs) using in vitro and in vivo approaches, finding that 5-HTR-mediated non-canonical G signalling is essential for hallucinogenic effect. We further presented five cryo-electron microscopy structures of 5-HTR-G/G in complex with psychedelics or nHAs. Structural analysis and pharmacological investigation revealed that a special contact between nHAs with 5-HTR mediated the signalling bias. Building on this insight, we identified a 2,5-dimethoxy-4-iodoamphetamine derivative, DOI-NBOMe, which exhibits potent and selective G-biased activity, and demonstrates promising therapeutic effects in mouse models without hallucinogenic effect. Our finding uncovers the functional mechanisms underlying the G signalling mediated by 5-HTR and provides valuable insights for designing psychedelic-based drugs with minimized risk from hallucinogenic effects.
History
DepositionJan 17, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63196.png

Downloads & links

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Map

FileDownload / File: emd_63196.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 300 pix.
= 225. Å		0.75 Å/pix.
x 300 pix.
= 225. Å		0.75 Å/pix.
x 300 pix.
= 225. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.092
Minimum - Maximum-0.8206917 - 1.2824003
Average (Standard dev.)-0.00040628822 (±0.025426224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 225.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63196_additional_1.map
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Half map: #2

Fileemd_63196_half_map_1.map
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Half map: #1

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Sample components

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Entire : 5-HT2AR-bound DOI in complex with Gi heterotrimer

EntireName: 5-HT2AR-bound DOI in complex with Gi heterotrimer
Components
  • Complex: 5-HT2AR-bound DOI in complex with Gi heterotrimer
    • 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
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha
    • Protein or peptide: 5-hydroxytryptamine receptor 2A
  • Ligand: CHOLESTEROL
  • Ligand: (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)-~{N}-[(2-methoxyphenyl)methyl]propan-2-amine

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Supramolecule #1: 5-HT2AR-bound DOI in complex with Gi heterotrimer

SupramoleculeName: 5-HT2AR-bound DOI in complex with Gi heterotrimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.41693 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 KIWN

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

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Macromolecule #2: 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: 2 / 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

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

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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine n...

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha
type: protein_or_peptide / ID: 3
Details: the aa 1-19 and 61-180 are chimera of Guanine nucleotide-binding protein G(i) subunit alpha-1; the aa 20-60 and 181-346 are chimera of Guanine nucleotide-binding protein G(s) subunit alpha; ...Details: the aa 1-19 and 61-180 are chimera of Guanine nucleotide-binding protein G(i) subunit alpha-1; the aa 20-60 and 181-346 are chimera of Guanine nucleotide-binding protein G(s) subunit alpha; the aa 347-361 are the C terminal (345-359) of Guanine nucleotide-binding protein G(q) subunit alpha.
Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.664285 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLSV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLSV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF KSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRKEFVDIST ASG DGRHIC YPHFTCSVDT ENARRIFNDC KDIILQMNLR EYNLV

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(i) subunit alpha-1, ...UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(q) subunit alpha

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Macromolecule #4: 5-hydroxytryptamine receptor 2A

MacromoleculeName: 5-hydroxytryptamine receptor 2A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.648945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDILCEENTS LSSTTNSLMQ LNDDTRLYSN DFNSGEANTS DAFNWTVDSE NRTNLSCEGC LSPSCLSLLH LQEKNWSALL TAVVIILTI AGNILVIMAV SLEKKLQNAT NYFLMSLAIA DMLLGFLVMP VSMLTILYGY RWPLPSKLCA VWIYLDVLFS T ASIMHLCA ...String:
MDILCEENTS LSSTTNSLMQ LNDDTRLYSN DFNSGEANTS DAFNWTVDSE NRTNLSCEGC LSPSCLSLLH LQEKNWSALL TAVVIILTI AGNILVIMAV SLEKKLQNAT NYFLMSLAIA DMLLGFLVMP VSMLTILYGY RWPLPSKLCA VWIYLDVLFS T ASIMHLCA ISLDRYVAIQ NPIHHSRFNS RTKAFLKIIA VWTISVGISM PIPVFGLQDD SKVFKEGSCL LADDNFVLIG SF VSFFIPL TIMVITYFLT IKSLQKEATL CVSDLGTRAK LASFSFLPQS SLSSEKLFQR SIHREPGSYT GRRTMQSISN EQK ACKVLG IVFFLFVVMW CPFFITNIMA VICKESCNED VIGALLNVFV WIGYLSSAVN PLVYTLFNKT YRSAFSRYIQ CQYK ENKKP LQLILVNTIP ALAYKSSQLQ MGQKKNSKQD AKTTDNDCSM VALGKQHSEE ASKDNSDGVN EKVSCV

UniProtKB: 5-hydroxytryptamine receptor 2A

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)-~{N}-[(2-methoxyphenyl...

MacromoleculeName: (2~{R})-1-(4-iodanyl-2,5-dimethoxy-phenyl)-~{N}-[(2-methoxyphenyl)methyl]propan-2-amine
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1ELA
Molecular weightTheoretical: 441.303 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 230771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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