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- EMDB-4358: Coupling specificity of heterotrimeric Go to the serotonin 5-HT1B... -

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Basic information

Entry
Database: EMDB / ID: EMD-4358
TitleCoupling specificity of heterotrimeric Go to the serotonin 5-HT1B receptor
Map dataMap after RELION "postprocessing" sharpened with a B=-200 and weighted by FSC.
Sample
  • Complex: Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer
    • Complex: 5-HT1B receptor
      • Protein or peptide: 5-hydroxytryptamine receptor 1B
    • Complex: Beta subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: mini-Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Gamma subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium
KeywordsG-protein coupled receptor / 5-HT1B / Mini-Go / serotonin / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of gamma-aminobutyric acid secretion / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / serotonergic synapse / Gi/o-coupled serotonin receptor activity / regulation of behavior / G protein-coupled serotonin receptor complex / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / Serotonin receptors ...negative regulation of gamma-aminobutyric acid secretion / voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / serotonergic synapse / Gi/o-coupled serotonin receptor activity / regulation of behavior / G protein-coupled serotonin receptor complex / negative regulation of synaptic transmission, GABAergic / response to mineralocorticoid / negative regulation of serotonin secretion / Serotonin receptors / serotonin receptor activity / drinking behavior / G protein-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / neurotransmitter receptor activity / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / bone remodeling / serotonin binding / vasoconstriction / negative regulation of synaptic transmission, glutamatergic / vesicle docking involved in exocytosis / G protein-coupled dopamine receptor signaling pathway / cellular response to alkaloid / regulation of synaptic vesicle exocytosis / regulation of heart contraction / parallel fiber to Purkinje cell synapse / regulation of dopamine secretion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / postsynaptic modulation of chemical synaptic transmission / negative regulation of insulin secretion / positive regulation of vascular associated smooth muscle cell proliferation / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / muscle contraction / presynaptic modulation of chemical synaptic transmission / calyx of Held / GABA-ergic synapse / locomotory behavior / response to cocaine / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / cellular response to xenobiotic stimulus / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / presynaptic membrane / G protein activity / cell body / GTPase binding / Ca2+ pathway / retina development in camera-type eye / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / response to ethanol / postsynaptic membrane / Ras protein signal transduction
Similarity search - Function
5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit ...5-Hydroxytryptamine 1B receptor / 5-hydroxytryptamine receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / 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. / WD domain, G-beta repeat / 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
Guanine nucleotide-binding protein G(O) subunit alpha-like / Guanine nucleotide-binding protein G(o) subunit alpha / 5-hydroxytryptamine receptor 1B / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsGarcia-Nafria J / Nehme R / Edwards P / Tate CG
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
European Research CouncilEMPSI 339995 United Kingdom
Medical Research Council (United Kingdom)MRC U105197215 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the serotonin 5-HT receptor coupled to heterotrimeric G.
Authors: Javier García-Nafría / Rony Nehmé / Patricia C Edwards / Christopher G Tate /
Abstract: G-protein-coupled receptors (GPCRs) form the largest family of receptors encoded by the human genome (around 800 genes). They transduce signals by coupling to a small number of heterotrimeric G ...G-protein-coupled receptors (GPCRs) form the largest family of receptors encoded by the human genome (around 800 genes). They transduce signals by coupling to a small number of heterotrimeric G proteins (16 genes encoding different α-subunits). Each human cell contains several GPCRs and G proteins. The structural determinants of coupling of G to four different GPCRs have been elucidated, but the molecular details of how the other G-protein classes couple to GPCRs are unknown. Here we present the cryo-electron microscopy structure of the serotonin 5-HT receptor (5-HTR) bound to the agonist donitriptan and coupled to an engineered G heterotrimer. In this complex, 5-HTR is in an active state; the intracellular domain of the receptor is in a similar conformation to that observed for the β-adrenoceptor (βAR) or the adenosine A receptor (AR) in complex with G. In contrast to the complexes with G, the gap between the receptor and the Gβ-subunit in the G-5-HTR complex precludes molecular contacts, and the interface between the Gα-subunit of G and the receptor is considerably smaller. These differences are likely to be caused by the differences in the interactions with the C terminus of the G α-subunit. The molecular variations between the interfaces of G and G in complex with GPCRs may contribute substantially to both the specificity of coupling and the kinetics of signalling.
History
DepositionApr 5, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseJun 20, 2018-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.07
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  • Surface view with fitted model
  • Atomic models: PDB-6g79
  • Surface level: 0.07
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4358.png

Downloads & links

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Map

FileDownload / File: emd_4358.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap after RELION "postprocessing" sharpened with a B=-200 and weighted by FSC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 150 pix.
= 159. Å		1.06 Å/pix.
x 150 pix.
= 159. Å		1.06 Å/pix.
x 150 pix.
= 159. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.19766203 - 0.34012505
Average (Standard dev.)0.0021200108 (±0.015749175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 158.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z159.000159.000159.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.1980.3400.002

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Supplemental data

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Sample components

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Entire : Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer

EntireName: Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer
Components
  • Complex: Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer
    • Complex: 5-HT1B receptor
      • Protein or peptide: 5-hydroxytryptamine receptor 1B
    • Complex: Beta subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: mini-Go
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Gamma subunit
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium

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Supramolecule #1: Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer

SupramoleculeName: Serotonin 5-HT1B receptor bound to a mini-Go heterotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.834 kDa/nm

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Supramolecule #2: 5-HT1B receptor

SupramoleculeName: 5-HT1B receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Beta subunit

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

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Supramolecule #4: mini-Go

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

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Supramolecule #5: Gamma subunit

SupramoleculeName: Gamma subunit / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2
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: 37.285734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW ...String:
SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NAICFFPNGN AF ATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGHDNRVSCL GVT DDGMAV ATGSWDSFLK IWN

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: 7.845078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI 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(o) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.155727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TLSAEERAAL ERSKAIEKNL KEDGISAAKD VKLLLLGADN SGKSTIVKQM KIIHGGSGGS GGTTGIVETH FTFKNLHFRL FDVGGQRSE RKKWIHCFED VTAIIFCVDL SDYNRMHESL MLFDSICNNK FFIDTSIILF LNKKDLFGEK IKKSPLTICF P EYTGPNTY ...String:
TLSAEERAAL ERSKAIEKNL KEDGISAAKD VKLLLLGADN SGKSTIVKQM KIIHGGSGGS GGTTGIVETH FTFKNLHFRL FDVGGQRSE RKKWIHCFED VTAIIFCVDL SDYNRMHESL MLFDSICNNK FFIDTSIILF LNKKDLFGEK IKKSPLTICF P EYTGPNTY EDAAAYIQAQ FESKNRSPNK EIYCHMTCAT DTNNAQVIFD AVTDIIIANN LRGCGLY

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha, Guanine nucleotide-binding protein G(O) subunit alpha-like

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Macromolecule #4: 5-hydroxytryptamine receptor 1B

MacromoleculeName: 5-hydroxytryptamine receptor 1B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.273375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAKDYIYQD SISLPWKVLL VMLLALITLA TTLSNAFVIA TVYRTRKLHT PANYLIASLA VTDLLVSILV MPISTMYTVT GRWTLGQVV CDFWLSSDIT CCTASIWHLC VIALDRYWAI TDAVEYSAKR TPKRAAVMIA LVWVFSISIS LPPFFWRQAK A EEEVSECV ...String:
MSAKDYIYQD SISLPWKVLL VMLLALITLA TTLSNAFVIA TVYRTRKLHT PANYLIASLA VTDLLVSILV MPISTMYTVT GRWTLGQVV CDFWLSSDIT CCTASIWHLC VIALDRYWAI TDAVEYSAKR TPKRAAVMIA LVWVFSISIS LPPFFWRQAK A EEEVSECV VNTDHILYTV YSTVGAFYFP TLLLIALYGR IYVEARSRIL KQTPNRTGKR LTRAQLITDS PGSTSSVTSI NS RVPDVPS ESGSPVYVNQ VKVRVSDALL EKKKLMAARE RKATKTLGII LGAFIVCWLP FFIISLVMPI CKDACWFHLA IFD FFTWLG YLNSLINPII YTMSNEDFKQ AFHKLIRFKC TSENLYFQ

UniProtKB: 5-hydroxytryptamine receptor 1B

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Macromolecule #5: 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]...

MacromoleculeName: 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium
type: ligand / ID: 5 / Number of copies: 1 / Formula: EP5
Molecular weightTheoretical: 404.485 Da
Chemical component information

ChemComp-EP5:
2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium / agonist*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

Concentration2.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMNaCl
1.0 mMMgCl2
0.15 %DDM
0.001 mMDonitriptan
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 5737 / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 730118
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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