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- EMDB-32268: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32268
TitleCryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
Map data
Sample
  • Complex: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
    • Complex: Guanine nucleotide-binding protein G(o) subunit alpha, Growth hormone secretagogue receptor type 1
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Guanine nucleotide-binding protein
      • Protein or peptide: Growth hormone secretagogue receptor type 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)/G(S)/G(T) subunit beta-1
    • Complex: ScFv16
      • Protein or peptide: ScFv16
    • Complex: Appetite-regulating hormone
      • Protein or peptide: Appetite-regulating hormone
  • Ligand: CHOLESTEROL
Function / homology
Function and homology information


positive regulation of bone development / positive regulation of gastric mucosal blood circulation / ghrelin receptor binding / negative regulation of locomotion / cortisol secretion / growth hormone secretagogue receptor activity / regulation of hindgut contraction / growth hormone-releasing hormone activity / negative regulation of circadian sleep/wake cycle, REM sleep / regulation of growth hormone secretion ...positive regulation of bone development / positive regulation of gastric mucosal blood circulation / ghrelin receptor binding / negative regulation of locomotion / cortisol secretion / growth hormone secretagogue receptor activity / regulation of hindgut contraction / growth hormone-releasing hormone activity / negative regulation of circadian sleep/wake cycle, REM sleep / regulation of growth hormone secretion / positive regulation of small intestinal transit / regulation of response to food / 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 / positive regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of cortisol secretion / positive regulation of corticotropin secretion / positive regulation of growth rate / ghrelin secretion / neuronal dense core vesicle lumen / gastric acid 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 / positive regulation of growth hormone secretion / adult feeding behavior / positive regulation of growth hormone receptor signaling pathway / negative regulation of appetite / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / actin polymerization or depolymerization / positive regulation of multicellular organism growth / cellular response to thyroid hormone stimulus / cartilage development / vesicle docking involved in exocytosis / response to growth hormone / regulation of postsynapse organization / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of synapse assembly / positive regulation of vascular endothelial cell proliferation / response to L-glutamate / G protein-coupled dopamine receptor signaling pathway / negative regulation of interleukin-1 beta production / cellular response to insulin-like growth factor stimulus / response to food / positive regulation of fatty acid metabolic process / response to dexamethasone / regulation of synapse assembly / regulation of heart contraction / parallel fiber to Purkinje cell synapse / positive regulation of sprouting angiogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of endothelial cell proliferation / dendrite development / negative regulation of interleukin-6 production / peptide hormone binding / protein tyrosine kinase activator activity / decidualization / negative regulation of tumor necrosis factor production / response to electrical stimulus / Synthesis, secretion, and deacylation of Ghrelin / postsynaptic modulation of chemical synaptic transmission / positive regulation of insulin secretion involved in cellular response to glucose stimulus / synapse assembly / response to hormone / hormone-mediated signaling pathway / positive regulation of adipose tissue development / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / muscle contraction / insulin-like growth factor receptor signaling pathway / negative regulation of angiogenesis / Peptide ligand-binding receptors / excitatory postsynaptic potential / locomotory behavior / synaptic membrane / G protein-coupled receptor binding / negative regulation of insulin secretion / G protein-coupled receptor activity / GABA-ergic synapse / positive regulation of insulin secretion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / G-protein beta/gamma-subunit complex binding / response to estrogen / 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 / G protein-coupled acetylcholine receptor signaling pathway / cellular response to insulin stimulus
Similarity search - Function
Preproghrelin peptide / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Growth hormone secretagogue receptor/motilin receptor / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit ...Preproghrelin peptide / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Motilin/ghrelin-associated peptide / Motilin/ghrelin / Growth hormone secretagogue receptor/motilin receptor / G-protein alpha subunit, group I / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
G protein subunit alpha o1 / 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 / Growth hormone secretagogue receptor type 1 / Appetite-regulating hormone
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsQin J / Ming Q / Ji S / Mao C / Shen D / Zhang Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of agonism and inverse agonism in ghrelin receptor.
Authors: Jiao Qin / Ye Cai / Zheng Xu / Qianqian Ming / Su-Yu Ji / Chao Wu / Huibing Zhang / Chunyou Mao / Dan-Dan Shen / Kunio Hirata / Yanbin Ma / Wei Yan / Yan Zhang / Zhenhua Shao /
Abstract: Much effort has been invested in the investigation of the structural basis of G protein-coupled receptors (GPCRs) activation. Inverse agonists, which can inhibit GPCRs with constitutive activity, are ...Much effort has been invested in the investigation of the structural basis of G protein-coupled receptors (GPCRs) activation. Inverse agonists, which can inhibit GPCRs with constitutive activity, are considered useful therapeutic agents, but the molecular mechanism of such ligands remains insufficiently understood. Here, we report a crystal structure of the ghrelin receptor bound to the inverse agonist PF-05190457 and a cryo-electron microscopy structure of the active ghrelin receptor-Go complex bound to the endogenous agonist ghrelin. Our structures reveal a distinct binding mode of the inverse agonist PF-05190457 in the ghrelin receptor, different from the binding mode of agonists and neutral antagonists. Combining the structural comparisons and cellular function assays, we find that a polar network and a notable hydrophobic cluster are required for receptor activation and constitutive activity. Together, our study provides insights into the detailed mechanism of ghrelin receptor binding to agonists and inverse agonists, and paves the way to design specific ligands targeting ghrelin receptors.
History
DepositionNov 24, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7w2z
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32268.png

Downloads & links

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Map

FileDownload / File: emd_32268.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 192 pix.
= 194.688 Å		1.01 Å/pix.
x 192 pix.
= 194.688 Å		1.01 Å/pix.
x 192 pix.
= 194.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.1723361 - 0.24205774
Average (Standard dev.)-3.161638e-05 (±0.0077345828)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1720.242-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go ...

EntireName: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
Components
  • Complex: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
    • Complex: Guanine nucleotide-binding protein G(o) subunit alpha, Growth hormone secretagogue receptor type 1
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Complex: Guanine nucleotide-binding protein
      • Protein or peptide: Growth hormone secretagogue receptor type 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)/G(S)/G(T) subunit beta-1
    • Complex: ScFv16
      • Protein or peptide: ScFv16
    • Complex: Appetite-regulating hormone
      • Protein or peptide: Appetite-regulating hormone
  • Ligand: CHOLESTEROL

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Supramolecule #1: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go ...

SupramoleculeName: Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightExperimental: 160.4 MDa

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Supramolecule #2: Guanine nucleotide-binding protein G(o) subunit alpha, Growth hor...

SupramoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha, Growth hormone secretagogue receptor type 1
type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Guanine nucleotide-binding protein

SupramoleculeName: Guanine nucleotide-binding protein / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3, #5
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: ScFv16

SupramoleculeName: ScFv16 / type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #5: Appetite-regulating hormone

SupramoleculeName: Appetite-regulating hormone / type: complex / Chimera: Yes / ID: 5 / Parent: 1 / Macromolecule list: #6

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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: 26.4561 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYDQVLHE DETTNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE K IKKSPLTI ...String:
MTLSAEERAA LERSKAIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYDQVLHE DETTNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE K IKKSPLTI CFPEYTGPNT YEDAAAYIQA QFESKNRSPN KEIYCHMTCA TDTNNAQVIF DAVTDIIIAN NLRGCGLY

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Macromolecule #2: Growth hormone secretagogue receptor type 1

MacromoleculeName: Growth hormone secretagogue receptor type 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.364309 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG NLLTMLVVSR FRELRTTTNL YLSSMAFSD LLIFLCMPLD LVRLWQYRPW NFGDLLCKLF QFVSESCTYA TVLTITALSV ERYFAICFPL RAKVVVTKGR V KLVIFVIW ...String:
MWNATPSEEP GFNLTLADLD WDASPGNDSL GDELLQLFPA PLLAGVTATC VALFVVGIAG NLLTMLVVSR FRELRTTTNL YLSSMAFSD LLIFLCMPLD LVRLWQYRPW NFGDLLCKLF QFVSESCTYA TVLTITALSV ERYFAICFPL RAKVVVTKGR V KLVIFVIW AVAFCSAGPI FVLVGVEHEN GTDPWDTNEC RPTEFAVRSG LLTVMVWVSS IFFFLPVFCL TVLYSLIGRK LW RRRRGDA VVGASLRDQN HKQTVKMLAV VVFAFILCWL PFHVGRYLFS KSFEPGSLEI AQISQYCNLV SFVLFYLSAA INP ILYNIM SKKYRVAVFR LLGFEPFSQR KLSTLKDESS RAWTESSINT

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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: ScFv16

MacromoleculeName: ScFv16 / type: protein_or_peptide / ID: 4 / 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 #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.285734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

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Macromolecule #6: Appetite-regulating hormone

MacromoleculeName: Appetite-regulating hormone / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.998288 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString:
GS(K4Q)FLSPEHQ RVQQRK

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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:

6ko5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 230306
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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