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- EMDB-36627: Cryo-EM structure of the anamorelin-bound ghrelin receptor and Gq... -

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Entry
Database: EMDB / ID: EMD-36627
TitleCryo-EM structure of the anamorelin-bound ghrelin receptor and Gq complex
Map data
Sample
  • Complex: Anamorelin-bound ghrelin receptor in complex with Gq
    • Protein or peptide: Engineered G-alpha-q
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: scFv16
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nb35
    • Protein or peptide: Growth hormone secretagogue receptor type 1
  • Ligand: 2-azanyl-N-[(2R)-1-[(3R)-3-[dimethylamino(methyl)carbamoyl]-3-(phenylmethyl)piperidin-1-yl]-3-(1H-indol-3-yl)-1-oxidanylidene-propan-2-yl]-2-methyl-propanamide
KeywordsGPCR / SBDD / Cachexia / MEMBRANE PROTEIN
Function / homology
Function and homology information


growth hormone secretagogue receptor activity / regulation of hindgut contraction / regulation of growth hormone secretion / positive regulation of small intestinal transit / negative regulation of locomotion involved in locomotory behavior / growth hormone-releasing hormone receptor activity / regulation of gastric motility / response to follicle-stimulating hormone / regulation of transmission of nerve impulse / ghrelin secretion ...growth hormone secretagogue receptor activity / regulation of hindgut contraction / regulation of growth hormone secretion / positive regulation of small intestinal transit / negative regulation of locomotion involved in locomotory behavior / growth hormone-releasing hormone receptor activity / regulation of gastric motility / response to follicle-stimulating hormone / regulation of transmission of nerve impulse / ghrelin secretion / positive regulation of appetite / growth hormone secretion / negative regulation of norepinephrine secretion / positive regulation of small intestine smooth muscle contraction / negative regulation of macrophage apoptotic process / positive regulation of eating behavior / adult feeding behavior / negative regulation of appetite / actin polymerization or depolymerization / positive regulation of multicellular organism growth / cellular response to thyroid hormone stimulus / response to growth hormone / regulation of postsynapse organization / positive regulation of insulin-like growth factor receptor signaling pathway / response to L-glutamate / positive regulation of vascular endothelial cell proliferation / negative regulation of interleukin-1 beta production / response to food / positive regulation of fatty acid metabolic process / response to dexamethasone / cellular response to insulin-like growth factor stimulus / regulation of synapse assembly / positive regulation of sprouting angiogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / decidualization / peptide hormone binding / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / postsynaptic modulation of chemical synaptic transmission / response to hormone / hormone-mediated signaling pathway / insulin-like growth factor receptor signaling pathway / Peptide ligand-binding receptors / synaptic membrane / negative regulation of insulin secretion / G protein-coupled receptor activity / negative regulation of inflammatory response / Schaffer collateral - CA1 synapse / 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 / cellular response to insulin stimulus / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / response to estradiol / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / cellular response to lipopolysaccharide / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / spermatogenesis / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction
Similarity search - Function
Growth hormone secretagogue receptor/motilin receptor / 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 ...Growth hormone secretagogue receptor/motilin receptor / 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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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
Similarity search - Domain/homology
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 / Growth hormone secretagogue receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsIm D / Shimura Y / Asada H / Iwata S
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K16217, 20K06531, 20KK0359, 22KK0099 Japan
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: The structure and function of the ghrelin receptor coding for drug actions.
Authors: Yuki Shiimura / Dohyun Im / Ryosuke Tany / Hidetsugu Asada / Ryoji Kise / Eon Kurumiya / Hideko Wakasugi-Masuho / Satoshi Yasuda / Kazuma Matsui / Jun-Ichi Kishikawa / Takayuki Kato / ...Authors: Yuki Shiimura / Dohyun Im / Ryosuke Tany / Hidetsugu Asada / Ryoji Kise / Eon Kurumiya / Hideko Wakasugi-Masuho / Satoshi Yasuda / Kazuma Matsui / Jun-Ichi Kishikawa / Takayuki Kato / Takeshi Murata / Masayasu Kojima / So Iwata / Ikuo Masuho /
Abstract: Drugs targeting the ghrelin receptor hold therapeutic potential in anorexia, obesity and diabetes. However, developing effective drugs is challenging. To tackle this common issue across a broad drug ...Drugs targeting the ghrelin receptor hold therapeutic potential in anorexia, obesity and diabetes. However, developing effective drugs is challenging. To tackle this common issue across a broad drug target, this study aims to understand how anamorelin, the only approved drug targeting the ghrelin receptor, operates compared to other synthetic drugs. Our research elucidated the receptor's structure with anamorelin and miniG, unveiling anamorelin's superagonistic activity. We demonstrated that ligands with distinct chemical structures uniquely bind to the receptor, resulting in diverse conformations and biasing signal transduction. Moreover, our study showcased the utility of structural information in effectively identifying natural genetic variations altering drug action and causing severe functional deficiencies, offering a basis for selecting the right medication on the basis of the individual's genomic sequence. Thus, by building on structural analysis, this study enhances the foundational framework for selecting therapeutic agents targeting the ghrelin receptor, by effectively leveraging signaling bias and genetic variations.
History
DepositionJun 20, 2023-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36627.png

Downloads & links

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Map

FileDownload / File: emd_36627.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesX (Sec.)Y (Row.)Z (Col.)
0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å		0.88 Å/pix.
x 320 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
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Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-42.917450000000002 - 63.638750000000002
Average (Standard dev.)0.000000000004984 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36627_additional_1.map
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Half map: #1

Fileemd_36627_half_map_1.map
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Half map: #2

Fileemd_36627_half_map_2.map
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Sample components

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Entire : Anamorelin-bound ghrelin receptor in complex with Gq

EntireName: Anamorelin-bound ghrelin receptor in complex with Gq
Components
  • Complex: Anamorelin-bound ghrelin receptor in complex with Gq
    • Protein or peptide: Engineered G-alpha-q
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: scFv16
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nb35
    • Protein or peptide: Growth hormone secretagogue receptor type 1
  • Ligand: 2-azanyl-N-[(2R)-1-[(3R)-3-[dimethylamino(methyl)carbamoyl]-3-(phenylmethyl)piperidin-1-yl]-3-(1H-indol-3-yl)-1-oxidanylidene-propan-2-yl]-2-methyl-propanamide

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Supramolecule #1: Anamorelin-bound ghrelin receptor in complex with Gq

SupramoleculeName: Anamorelin-bound ghrelin receptor in complex with Gq / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#6, #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 190 KDa

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Macromolecule #1: Growth hormone secretagogue receptor type 1

MacromoleculeName: Growth hormone secretagogue receptor type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.82702 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WNATPSEEPG FNLTLADLDW DASPGNDSLG DELLQLFPAP LLAGVTATCV ALFVVGIAGN LLTMLVVSRF RELRTTTNLY LSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV K LVIFVIWA ...String:
WNATPSEEPG FNLTLADLDW DASPGNDSLG DELLQLFPAP LLAGVTATCV ALFVVGIAGN LLTMLVVSRF RELRTTTNLY LSSMAFSDL LIFLCMPLDL VRLWQYRPWN FGDLLCKLFQ FVSESCTYAT VLTITALSVE RYFAICFPLR AKVVVTKGRV K LVIFVIWA VAFCSAGPIF VLVGVEHENG TDPWDTNECR PTEFAVRSGL LTVMVWVSSI FFFLPVFCLT VLYSLIGRKL WR RRRGDAV VGASLRDQNH KQTVKMLAVV VFAFILCWLP FHVGRYLFSK SFEPGSLEIA QISQYCNLVS FVLFYLSAAI NPI LYNIMS KKYRVAVFRL LGFEPFSQRK LSTLKDESSR AWTESSINTV FTLEDFVGDW EQTAAYNLDQ VLEQGGVSSL LQNL AVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNMLNY FGRPY EGIA VFDGKKITVT GTLWNGNKII DERLITPDGS MLFRVTINS

UniProtKB: Growth hormone secretagogue receptor type 1

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Macromolecule #2: Engineered G-alpha-q

MacromoleculeName: Engineered G-alpha-q / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.724383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV 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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.282156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HLEVLFQGPG SSGSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAKI YAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR E LAGHTGYL ...String:
MHHHHHHHHH HLEVLFQGPG SSGSELDQLR QEAEQLKNQI RDARKACADA TLSQITNNID PVGRIQMRTR RTLRGHLAKI YAMHWGTDS RLLVSASQDG KLIIWDSYTT NKVHAIPLRS SWVMTCAYAP SGNYVACGGL DNICSIYNLK TREGNVRVSR E LAGHTGYL SCCRFLDDNQ IVTSSGDTTC ALWDIETGQQ TTTFTGHTGD VMSLSLAPDT RLFVSGACDA SAKLWDVREG MC RQTFTGH ESDINAICFF PNGNAFATGS DDATCRLFDL RADQELMTYS HDNIICGITS VSFSKSGRLL LAGYDDFNCN VWD ALKADR AGVLAGHDNR VSCLGVTDDG MAVATGSWDS FLKIWNGSSG GGGSGGGGSS GVSGWRLFKK IS

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

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Macromolecule #4: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.784896 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 KAAAHHHHHH HH

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Macromolecule #5: 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: 5 / 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 #6: Nb35

MacromoleculeName: Nb35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.016636 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MQVQLQESGG GLVQPGGSLR LSCAASGFTF SNYKMNWVRQ APGKGLEWVS DISQSGASIS YTGSVKGRFT ISRDNAKNTL YLQMNSLKP EDTAVYYCAR CPAPFTRDCF DVTSTTYAYR GQGTQVTVSS

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Macromolecule #7: 2-azanyl-N-[(2R)-1-[(3R)-3-[dimethylamino(methyl)carbamoyl]-3-(ph...

MacromoleculeName: 2-azanyl-N-[(2R)-1-[(3R)-3-[dimethylamino(methyl)carbamoyl]-3-(phenylmethyl)piperidin-1-yl]-3-(1H-indol-3-yl)-1-oxidanylidene-propan-2-yl]-2-methyl-propanamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: UYI
Molecular weightTheoretical: 546.704 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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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:

7f9y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 500563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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