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- EMDB-20612: GPCR-Beta arrestin structure in lipid bilayer -

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Basic information

Entry
Database: EMDB / ID: EMD-20612
TitleGPCR-Beta arrestin structure in lipid bilayer
Map dataGPCR-Beta arrestin structure in lipid bilayer
Sample
  • Complex: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30).
    • Complex: Phosphorylated human muscarinic acetylcholine receptor M2
      • Protein or peptide: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera
    • Complex: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393
      • Protein or peptide: Beta-arrestin-1
    • Complex: Antibody Fragment (Fab30)
      • Protein or peptide: Fab30 heavy chain
      • Protein or peptide: Fab30 light chain
  • Ligand: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide
KeywordsArrestin / GPCR / complex / signaling / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / sensory perception of touch / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / renal water retention ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / sensory perception of touch / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / protein phosphorylated amino acid binding / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Lysosome Vesicle Biogenesis / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / Ub-specific processing proteases / regulation of inositol trisphosphate biosynthetic process / AP-2 adaptor complex binding / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / renal water absorption / angiotensin receptor binding / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / cholinergic synapse / hemostasis / Cargo recognition for clathrin-mediated endocytosis / regulation of smooth muscle contraction / Clathrin-mediated endocytosis / telencephalon development / clathrin-cargo adaptor activity / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / mitogen-activated protein kinase kinase binding / sensory perception / Thrombin signalling through proteinase activated receptors (PARs) / clathrin binding / stress fiber assembly / response to morphine / regulation of heart contraction / positive regulation of Rho protein signal transduction / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / pseudopodium / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / positive regulation of vasoconstriction / phototransduction / negative regulation of Notch signaling pathway / endocytic vesicle / immunoglobulin complex / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cysteine-type endopeptidase inhibitor activity / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / response to cytokine / negative regulation of protein ubiquitination / presynaptic modulation of chemical synaptic transmission / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / GTPase activator activity / clathrin-coated endocytic vesicle membrane / phosphoprotein binding / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to virus / endocytosis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / nervous system development / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynapse / cytoplasmic vesicle / regulation of apoptotic process / G alpha (i) signalling events / G alpha (s) signalling events / molecular adaptor activity / dendritic spine / basolateral plasma membrane / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / negative regulation of neuron apoptotic process / adaptive immune response / transmembrane transporter binding / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of ERK1 and ERK2 cascade
Similarity search - Function
Muscarinic acetylcholine receptor M2 / Vasopressin V2 receptor / Vasopressin receptor / Muscarinic acetylcholine receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Muscarinic acetylcholine receptor M2 / Vasopressin V2 receptor / Vasopressin receptor / Muscarinic acetylcholine receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / : / : / Serpentine type 7TM GPCR chemoreceptor Srsx / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / G-protein coupled receptors family 1 signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Immunoglobulin E-set / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Muscarinic acetylcholine receptor M2 / Beta-arrestin-1 / Vasopressin V2 receptor / Ig-like domain-containing protein / Epididymis luminal protein 214
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsStaus DP / Hu H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL16037 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS092695 United States
CitationJournal: Nature / Year: 2020
Title: Structure of the M2 muscarinic receptor-β-arrestin complex in a lipid nanodisc.
Authors: Dean P Staus / Hongli Hu / Michael J Robertson / Alissa L W Kleinhenz / Laura M Wingler / William D Capel / Naomi R Latorraca / Robert J Lefkowitz / Georgios Skiniotis /
Abstract: After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β- ...After activation by an agonist, G-protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G-protein signalling and promotes receptor endocytosis. Additionally, β-arrestin directly regulates many cell signalling pathways that can induce cellular responses distinct from that of G proteins. In contrast to G proteins, for which there are many high-resolution structures in complex with GPCRs, the molecular mechanisms underlying the interaction of β-arrestin with GPCRs are much less understood. Here we present a cryo-electron microscopy structure of β-arrestin 1 (βarr1) in complex with M2 muscarinic receptor (M2R) reconstituted in lipid nanodiscs. The M2R-βarr1 complex displays a multimodal network of flexible interactions, including binding of the N domain of βarr1 to phosphorylated receptor residues and insertion of the finger loop of βarr1 into the M2R seven-transmembrane bundle, which adopts a conformation similar to that in the M2R-heterotrimeric G protein complex. Moreover, the cryo-electron microscopy map reveals that the C-edge of βarr1 engages the lipid bilayer. Through atomistic simulations and biophysical, biochemical and cellular assays, we show that the C-edge is critical for stable complex formation, βarr1 recruitment, receptor internalization, and desensitization of G-protein activation. Taken together, these data suggest that the cooperative interactions of β-arrestin with both the receptor and the phospholipid bilayer contribute to its functional versatility.
History
DepositionAug 16, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseFeb 26, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / 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
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  • 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-6u1n
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20612.png

Downloads & links

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Map

FileDownload / File: emd_20612.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGPCR-Beta arrestin structure in lipid bilayer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 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: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.06625173 - 0.14013499
Average (Standard dev.)0.00024197591 (±0.0036906875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0660.1400.000

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Supplemental data

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Sample components

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Entire : Phosphorylated human muscarinic acetylcholine receptor M2 in comp...

EntireName: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30).
Components
  • Complex: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30).
    • Complex: Phosphorylated human muscarinic acetylcholine receptor M2
      • Protein or peptide: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera
    • Complex: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393
      • Protein or peptide: Beta-arrestin-1
    • Complex: Antibody Fragment (Fab30)
      • Protein or peptide: Fab30 heavy chain
      • Protein or peptide: Fab30 light chain
  • Ligand: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide

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Supramolecule #1: Phosphorylated human muscarinic acetylcholine receptor M2 in comp...

SupramoleculeName: Phosphorylated human muscarinic acetylcholine receptor M2 in complex with rat beta-arrestin1, stabilized by an antibody fragment (Fab30).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Phosphorylated human muscarinic acetylcholine receptor M2

SupramoleculeName: Phosphorylated human muscarinic acetylcholine receptor M2
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Phosphorylated M2R was generated by ligating a synthetic phosphopeptide derived from the vasopressin-2-receptor (V2Rpp) using the enzyme sortase.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393

SupramoleculeName: Cysteine-free rat beta-arrestin 1 truncated at amino acid 393
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #4: Antibody Fragment (Fab30)

SupramoleculeName: Antibody Fragment (Fab30) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera

MacromoleculeName: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor chimera
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.616176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF ...String:
DYKDDDDKNN STNSSNNSLA LTSPYKTFEV VFIVLVAGSL SLVTIIGNIL VMVSIKVNRH LQTVNNYFLF SLACADLIIG VFSMNLYTL YTVIGYWPLG PVVCDLWLAL DYVVSNASVM NLLIISFDRY FCVTKPLTYP VKRTTKMAGM MIAAAWVLSF I LWAPAILF WQFIVGVRTV EDGECYIQFF SNAAVTFGTA IAAFYLPVII MTVLYWHISR ASKSRIKKDK KEPVANQDPV SP SLVQGRI VKPNNNNMPS SDDGLEHNKI QNGKAPRDPV TENCVQGEEK ESSNDSTSVS AVASNMRDDE ITQDENTVST SLG HSKDEN SKQTCIRIGT KTPKSDSCTP TNTTVEVVGS SGQNGDEKQN IVARKIVKMT KQPAKKKPPP SREKKVTRTI LAIL LAFII TWAPYNVMVL INTFCAPCIP NTVWTIGYWL CYINSTINPA CYALCNATFK KTFKHLLMCH YKNIGATRLP ETGGG ARGR TPPSLGPQDE (SEP)C(TPO)(TPO)A(SEP)(SEP)(SEP)LA KDTSS

UniProtKB: Muscarinic acetylcholine receptor M2, Vasopressin V2 receptor

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Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 45.01718 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK ...String:
GSPEFPGRLG DKGTRVFKKA SPNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTVAFR YGREDLDVLG LTFRKDLFV ANVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPSSVTLQP GPEDTGKALG VDYEVKAFVA E NLEEKIHK RNSVRLVIRK VQYAPERPGP QPTAETTRQF LMSDKPLHLE ASLDKEIYYH GEPISVNVHV TNNTNKTVKK IK ISVRQYA DIVLFNTAQY KVPVAMEEAD DTVAPSSTFS KVYTLTPFLA NNREKRGLAL DGKLKHEDTN LASSTLLREG ANR EILGII VSYKVKVKLV VSRGGLLGDL ASSDVAVELP FTLMHPKPKE EPPHREVPES ETPVDTNLIE LDTNDDDIVF EDFA R

UniProtKB: Beta-arrestin-1

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Macromolecule #3: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.512354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH

UniProtKB: Epididymis luminal protein 214

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Macromolecule #4: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

UniProtKB: Ig-like domain-containing protein

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Macromolecule #5: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1...

MacromoleculeName: 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: 2CU
Molecular weightTheoretical: 437.944 Da
Chemical component information

ChemComp-2CU:
3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide

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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 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 47169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 47169
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

Particle selectionNumber selected: 11700000
Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 145618
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6u1n:
GPCR-Beta arrestin structure in lipid bilayer

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