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- PDB-9foj: LGTV TP21. Langat virus, strain TP21 -

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Basic information

Entry
Database: PDB / ID: 9foj
TitleLGTV TP21. Langat virus, strain TP21
Components
  • Envelope protein E
  • Small envelope protein M
KeywordsVIRUS / Flavivirus / Langat virus / recombinant virus
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated activation of host apoptosis / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-CPL / Genome polyprotein
Similarity search - Component
Biological speciesLangat virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsBisikalo, K. / Rosendal, E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-05851 Sweden
CitationJournal: Biorxiv / Year: 2024
Title: The influence of the pre-membrane and envelope proteins on structure, pathogenicity and tropism of tick-borne encephalitis virus
Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / ...Authors: Rosendal, E. / Bisikalo, K. / Willekens, S.M. / Lindgren, M. / Holoubek, J. / Svoboda, P. / Lappalainen, A. / Konighofer, E. / Mirgorodskaya, E. / Norden, R. / Morini, F. / Rosenbaum, W. / Ruzek, D. / Ahlgren, U. / Anastasina, M. / Merits, A. / Butcher, S.J. / Nilsson, E. / Overby, A.K.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / pdbx_modification_feature / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_admin.last_update / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,29415
Polymers185,4726
Non-polymers5,8229
Water00
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules

A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Small envelope protein M
E: Small envelope protein M
F: Small envelope protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,477,637900
Polymers11,128,343360
Non-polymers349,294540
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Envelope protein E


Mass: 53574.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus (strain TP21) / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: P29837
#2: Protein Small envelope protein M / Matrix protein


Mass: 8249.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langat virus (strain TP21) / Cell line (production host): A549 MAVS -/- / Production host: Homo sapiens (human) / References: UniProt: P29837
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Langat virus (strain TP21) / Type: VIRUS / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Langat virus (strain TP21)
Source (recombinant)Organism: Homo sapiens (human) / Cell: A549 MAVS -/-
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 500 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Details: VP-SFM growth medium, supplemented with rapamycin and glutamate.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Alignment procedure: BASIC
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1430

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14ISOLDEmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15306
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12857 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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