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- EMDB-38538: Cryo-EM structure of the tethered agonist-bound human PAR1-Gq complex -

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Entry
Database: EMDB / ID: EMD-38538
TitleCryo-EM structure of the tethered agonist-bound human PAR1-Gq complex
Map data
Sample
  • Complex: Cryo-EM structure of ligand-bound form of the receptor in complex with the transducer
    • Complex: G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Gi1-Gq chimeric
      • Protein or peptide: G subunit q (Gi1-Gq chimeric)
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: Proteinase-activated receptor 1
      • Protein or peptide: Proteinase-activated receptor 1 LgBiT
  • Ligand: CHOLESTEROL
KeywordsGPCR / MEMBRANE PROTEIN / protease-activated receptor
Function / homology
Function and homology information


negative regulation of renin secretion into blood stream / dendritic cell homeostasis / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / platelet dense tubular network / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor activity / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / cell-cell junction maintenance ...negative regulation of renin secretion into blood stream / dendritic cell homeostasis / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / platelet dense tubular network / establishment of synaptic specificity at neuromuscular junction / thrombin-activated receptor activity / regulation of interleukin-1 beta production / platelet dense granule organization / connective tissue replacement involved in inflammatory response wound healing / cell-cell junction maintenance / positive regulation of smooth muscle contraction / positive regulation of calcium ion transport / 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 / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (s) signalling events / G alpha (q) signalling events / spectrin binding / G alpha (i) signalling events / negative regulation of glomerular filtration / thrombin-activated receptor signaling pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of Rho protein signal transduction / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of blood coagulation / positive regulation of vasoconstriction / alkylglycerophosphoethanolamine phosphodiesterase activity / positive regulation of collagen biosynthetic process / anatomical structure morphogenesis / positive regulation of blood coagulation / G-protein alpha-subunit binding / photoreceptor outer segment / Common Pathway of Fibrin Clot Formation / release of sequestered calcium ion into cytosol / cardiac muscle cell apoptotic process / photoreceptor inner segment / homeostasis of number of cells within a tissue / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / G protein-coupled receptor activity / regulation of synaptic plasticity / caveola / platelet activation / positive regulation of interleukin-6 production / response to wounding / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / late endosome / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / cell body / GTPase binding
Similarity search - Function
Thrombin receptor / Protease-activated 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 ...Thrombin receptor / Protease-activated 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
Proteinase-activated receptor 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesRattus (rats) / Bos taurus (domestic cattle) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGuo J / Zhang Y / Shen Q / Zang S / Shen D / Zhang H / Chen Z / Wang G / Zhang C / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis of tethered agonism and G protein coupling of protease-activated receptors.
Authors: Jia Guo / Yun-Li Zhou / Yixin Yang / Shimeng Guo / Erli You / Xin Xie / Yi Jiang / Chunyou Mao / H Eric Xu / Yan Zhang /
Abstract: Protease-activated receptors (PARs) are a unique group within the G protein-coupled receptor superfamily, orchestrating cellular responses to extracellular proteases via enzymatic cleavage, which ...Protease-activated receptors (PARs) are a unique group within the G protein-coupled receptor superfamily, orchestrating cellular responses to extracellular proteases via enzymatic cleavage, which triggers intracellular signaling pathways. Protease-activated receptor 1 (PAR1) is a key member of this family and is recognized as a critical pharmacological target for managing thrombotic disorders. In this study, we present cryo-electron microscopy structures of PAR1 in its activated state, induced by its natural tethered agonist (TA), in complex with two distinct downstream proteins, the G and G heterotrimers, respectively. The TA peptide is positioned within a surface pocket, prompting PAR1 activation through notable conformational shifts. Contrary to the typical receptor activation that involves the outward movement of transmembrane helix 6 (TM6), PAR1 activation is characterized by the simultaneous downward shift of TM6 and TM7, coupled with the rotation of a group of aromatic residues. This results in the displacement of an intracellular anion, creating space for downstream G protein binding. Our findings delineate the TA recognition pattern and highlight a distinct role of the second extracellular loop in forming β-sheets with TA within the PAR family, a feature not observed in other TA-activated receptors. Moreover, the nuanced differences in the interactions between intracellular loops 2/3 and the Gα subunit of different G proteins are crucial for determining the specificity of G protein coupling. These insights contribute to our understanding of the ligand binding and activation mechanisms of PARs, illuminating the basis for PAR1's versatility in G protein coupling.
History
DepositionJan 2, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38538.png

Downloads & links

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Map

FileDownload / File: emd_38538.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214.2 Å		1.07 Å/pix.
x 200 pix.
= 214.2 Å		1.07 Å/pix.
x 200 pix.
= 214.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0131
Minimum - Maximum-0.034779064 - 0.09849829
Average (Standard dev.)0.00009493523 (±0.0037433691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38538_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38538_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of ligand-bound form of the receptor in complex...

EntireName: Cryo-EM structure of ligand-bound form of the receptor in complex with the transducer
Components
  • Complex: Cryo-EM structure of ligand-bound form of the receptor in complex with the transducer
    • Complex: G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: G(I)/G(S)/G(O) subunit gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Gi1-Gq chimeric
      • Protein or peptide: G subunit q (Gi1-Gq chimeric)
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: Proteinase-activated receptor 1
      • Protein or peptide: Proteinase-activated receptor 1 LgBiT
  • Ligand: CHOLESTEROL

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Supramolecule #1: Cryo-EM structure of ligand-bound form of the receptor in complex...

SupramoleculeName: Cryo-EM structure of ligand-bound form of the receptor in complex with the transducer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Rattus (rats)

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Supramolecule #2: G(I)/G(S)/G(T) subunit beta-1

SupramoleculeName: G(I)/G(S)/G(T) subunit beta-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: G(I)/G(S)/G(O) subunit gamma-2

SupramoleculeName: G(I)/G(S)/G(O) subunit gamma-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Gi1-Gq chimeric

SupramoleculeName: Gi1-Gq chimeric / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #5: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Proteinase-activated receptor 1

SupramoleculeName: Proteinase-activated receptor 1 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5

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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: Rattus (rats)
Molecular weightTheoretical: 41.332137 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSGWRLFKK ISGSSGGGGS GGGGSSGGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKI YAMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT R EGNVRVSR ...String:
MVSGWRLFKK ISGSSGGGGS GGGGSSGGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKI YAMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT R EGNVRVSR ELAGHTGYLS CCRFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AK LWDVREG MCRQTFTGHE SDINAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGY DDFNCN VWDALKADRA GVLAGHDNRV SCLGVTDDGM AVATGSWDSF LKIWNHHHHH HHH

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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.432554 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFC

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

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Macromolecule #3: G subunit q (Gi1-Gq chimeric)

MacromoleculeName: G subunit q (Gi1-Gq chimeric) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.708383 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 YPHFTCAVDT ENARRIFNDC KDIILQMNLR EYNLV

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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: 32.561281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFAVQL VESGGGLVQP GGSRKLSCSA SGFAFSSFGM HWVRQAPEKG LEWVAYISS GSGTIYYADT VKGRFTISRD DPKNTLFLQM TSLRSEDTAM YYCVRSIYYY GSSPFDFWGQ GTTLTVSAGG G GSGGGGSG ...String:
LLVNQSHQGF NKEHTSKMVS AIVLYVLLAA AAHSAFAVQL VESGGGLVQP GGSRKLSCSA SGFAFSSFGM HWVRQAPEKG LEWVAYISS GSGTIYYADT VKGRFTISRD DPKNTLFLQM TSLRSEDTAM YYCVRSIYYY GSSPFDFWGQ GTTLTVSAGG G GSGGGGSG GGGSADIVMT QATSSVPVTP GESVSISCRS SKSLLHSNGN TYLYWFLQRP GQSPQLLIYR MSNLASGVPD RF SGSGSGT AFTLTISRLE AEDVGVYYCM QHLEYPLTFG AGTKLELVDE NLYFQGASHH HHHHHH

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Macromolecule #5: Proteinase-activated receptor 1 LgBiT

MacromoleculeName: Proteinase-activated receptor 1 LgBiT / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.787539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SFLLRNPNDK YEPFWEDEEK NESGLTEYRL VSINKSSPLQ KQLPAFISED ASGYLTSSWL TLFVPSVYTG VFVVSLPLNI MAIVVFILK MKVKKPAVVY MLHLATADVL FVSVLPFKIS YYFSGSDWQF GSELCRFVTA AFYCNMYASI LLMTVISIDR F LAVVYPMQ ...String:
SFLLRNPNDK YEPFWEDEEK NESGLTEYRL VSINKSSPLQ KQLPAFISED ASGYLTSSWL TLFVPSVYTG VFVVSLPLNI MAIVVFILK MKVKKPAVVY MLHLATADVL FVSVLPFKIS YYFSGSDWQF GSELCRFVTA AFYCNMYASI LLMTVISIDR F LAVVYPMQ SLSWRTLGRA SFTCLAIWAL AIAGVVPLLL KEQTIQVPGL NITTCHDVLN ETLLEGYYAY YFSAFSAVFF FV PLIISTV CYVSIIRCLS SSAVANRSKK SRALFLSAAV FCIFIICFGP TNVLLIAHYS FLSHTSTTEA AYFAYLLCVC VSS ISCCID PLIYYYASSE CQRYVYSILC CKESSDPSSY GSSGGGGSGG GGSSGVFTLE DFVGDWEQTA AYNLDQVLEQ GGVS SLLQN LAVSVTPIQR IVRSGENALK IDIHVIIPYE GLSADQMAQI EEVFKVVYPV DDHHFKVILP YGTLVIDGVT PNMLN YFGR PYEGIAVFDG KKITVTGTLW NGNKIIDERL ITPDGSMLFR VTINSGGS

UniProtKB: Proteinase-activated receptor 1

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 6 / 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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Frames/image: 1-40 / Number real images: 5048 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49310 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
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: PDB ENTRY
PDB model - PDB ID:

3vw7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 723778
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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