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- EMDB-65949: D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815 -

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Basic information

Entry
Database: EMDB / ID: EMD-65949
TitleD1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
Map data
Sample
  • Complex: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815
    • Protein or peptide: x 5 types
  • Ligand: x 6 types
Keywordsagonist / PAM / GPCR / STRUCTURAL PROTEIN
Function / homology
Function and homology information


dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / G protein-coupled receptor complex ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / G protein-coupled receptor complex / modification of postsynaptic structure / adult walking behavior / positive regulation of potassium ion transport / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / non-motile cilium / arrestin family protein binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / AMPA selective glutamate receptor signaling pathway / G alpha (z) signalling events / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / norepinephrine binding / G protein-coupled dopamine receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenoceptors / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / positive regulation of lipophagy / positive regulation of cardiac muscle cell contraction / G alpha (i) signalling events / mating behavior / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / negative regulation of G protein-coupled receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / regulation of smooth muscle contraction / Ca2+ pathway / G alpha (z) signalling events / ciliary membrane / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G alpha (q) signalling events / G alpha (s) signalling events / adrenergic receptor signaling pathway / photoreceptor outer segment membrane / response to psychosocial stress / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (i) signalling events / dopamine metabolic process / endosome to lysosome transport / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / sensory perception of taste / positive regulation of glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / retina development in camera-type eye / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / transmission of nerve impulse / regulation of skeletal muscle contraction / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / developmental growth / hair follicle placode formation / PKA activation in glucagon signalling / renal water homeostasis / cardiac muscle cell apoptotic process / intracellular transport / potassium channel regulator activity / G-protein alpha-subunit binding
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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 ...Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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
Beta-2 adrenergic receptor / D(1A) dopamine receptor / 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)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat) / Bos taurus (domestic cattle) / Vicugna pacos (alpaca) / Oplophorus gracilirostris (arthropod)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsXu Y / Wang K / Zhuang Y / Xu HE
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130022 China
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)82495184 China
National Natural Science Foundation of China (NSFC)32401002 China
CitationJournal: To Be Published
Title: Molecular insights into the cooperative allosteric modulation of D1 dopamine receptor
Authors: Xu Y / Wang K / Zhuang Y
History
DepositionAug 22, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65949.png

Downloads & links

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Map

FileDownload / File: emd_65949.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.7544558 - 3.2361922
Average (Standard dev.)0.0002492419 (±0.08623875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 219.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65949_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_65949_half_map_2.map
Projections & Slices
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Sample components

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Entire : D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815

EntireName: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815
Components
  • Complex: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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: Nanobody35
    • Protein or peptide: Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit
  • Ligand: L-DOPAMINE
  • Ligand: ~{N}-(3-aminocarbonyl-6-~{tert}-butyl-1-benzothiophen-2-yl)pyridine-4-carboxamide
  • Ligand: 1-[(1~{S},3~{R},6~{R})-6-(1,3-benzodioxol-5-yl)-3-bicyclo[4.1.0]heptanyl]-4-[(2-bromanyl-5-chloranyl-phenyl)methyl]piperazine
  • Ligand: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815

SupramoleculeName: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / 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: 29.048932 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKMIEKQL QKDKQVYRAT HRLLLLGADN SGKSTIVKQM RIYHVNSGIF ETKFQVDKVN FHMFDVGAQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA ...String:
MGCLGNSKTE DQRNEEKAQR EANKMIEKQL QKDKQVYRAT HRLLLLGADN SGKSTIVKQM RIYHVNSGIF ETKFQVDKVN FHMFDVGAQ RDERRKWIQC FNDVTAIIFV VDSSDYNRLQ EALNDFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK I EDYFPEFA RYTTPEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCS VDTENARRIF NDCRDIIQRM HL RQYELL

UniProtKB: 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(s) subunit alpha isoforms short

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 40.226992 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWNG SSGGGGSGGG GSSGVSGWRL FKKIS

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

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.56375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

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

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Macromolecule #4: Nanobody35

MacromoleculeName: Nanobody35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 17.352498 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGR FTISRDNAKN TLYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHHEPE A

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Macromolecule #5: Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered opl...

MacromoleculeName: Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit
type: protein_or_peptide / ID: 5
Details: Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit: PDB ID: 7SNY
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oplophorus gracilirostris (arthropod)
Molecular weightTheoretical: 66.836758 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEA SRTLNTSAMD GTGLVVERD FSVRILTACF LSLLILSTLL GNTLVCAAVI RFRHLRSKVT NFFVISLAVS DLLVAVLVMP WKAVAEIAGF W PFGSFCNI ...String:
MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS DYKDDDDVDM GQPGNGSAFL LAPNGSHAPD HDVTQQRDEA SRTLNTSAMD GTGLVVERD FSVRILTACF LSLLILSTLL GNTLVCAAVI RFRHLRSKVT NFFVISLAVS DLLVAVLVMP WKAVAEIAGF W PFGSFCNI WVAFDIMCST ASILNLCVIS VDRYWAISSP FRYERKMTPK AAFILISVAW TLSVLISFIP VQLSWHKAKP TS PSDGNAT SLAETIDNCD SSLSRTYAIS SSVISFYIPV AIMIVTYTRI YRIAQKQIRR IAALERAAVH AKNCQTTTGN GKP VECSQP ESSFKMSFKR ETKVLKTLSV IMGVFVCCWL PFFILNCILP FCGSGETQPF CIDSNTFDVF VWFGWANSSL NPII YAFNA DFRKAFSTLL GCYRLCPATN NAIETVSINN NGVFTLEDFV GDWEQTAAYN LDQVLEQGGV SSLLQNLAVS VTPIQ RIVR SGENALKIDI HVIIPYEGLS ADQMAQIEEV FKVVYPVDDH HFKVILPYGT LVIDGVTPNM LNYFGRPYEG IAVFDG KKI TVTGTLWNGN KIIDERLITP DGSMLFRVTI NSHHHHHHHH

UniProtKB: Beta-2 adrenergic receptor, D(1A) dopamine receptor

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Macromolecule #6: L-DOPAMINE

MacromoleculeName: L-DOPAMINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: LDP
Molecular weightTheoretical: 153.178 Da
Chemical component information

ChemComp-LDP:
L-DOPAMINE / medication*YM

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Macromolecule #7: ~{N}-(3-aminocarbonyl-6-~{tert}-butyl-1-benzothiophen-2-yl)pyridi...

MacromoleculeName: ~{N}-(3-aminocarbonyl-6-~{tert}-butyl-1-benzothiophen-2-yl)pyridine-4-carboxamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1EWF
Molecular weightTheoretical: 353.438 Da

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Macromolecule #8: 1-[(1~{S},3~{R},6~{R})-6-(1,3-benzodioxol-5-yl)-3-bicyclo[4.1.0]h...

MacromoleculeName: 1-[(1~{S},3~{R},6~{R})-6-(1,3-benzodioxol-5-yl)-3-bicyclo[4.1.0]heptanyl]-4-[(2-bromanyl-5-chloranyl-phenyl)methyl]piperazine
type: ligand / ID: 8 / Number of copies: 1 / Formula: A1EV3
Molecular weightTheoretical: 503.859 Da

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Macromolecule #9: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methy...

MacromoleculeName: 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone
type: ligand / ID: 9 / Number of copies: 1 / Formula: G4C
Molecular weightTheoretical: 450.398 Da
Chemical component information

ChemComp-G4C:
2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone

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Macromolecule #10: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 10 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ljc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 209112
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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