+Open data
-Basic information
Entry | Database: PDB / ID: 8ppl | ||||||||||||||||||||||||||||||||||||||||||
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Title | MERS-CoV Nsp1 bound to the human 43S pre-initiation complex | ||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | TRANSLATION / Nsp1 / MERS / SARS / SARS-CoV2 / ribosome / 40S ribosomal subunit / translation inhibition / coronavirus / 43S PIC / 43S pre-initiation complex / mRNA channel / initiation factor / eIF2 / eIF3 / eIF1 / eIF1A / VIRAL PROTEIN | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / positive regulation of mRNA cis splicing, via spliceosome / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation ...male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / positive regulation of mRNA cis splicing, via spliceosome / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / translation reinitiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / regulation of translational initiation in response to stress / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Middle East respiratory syndrome-related coronavirus Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. ...Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | Switzerland, United States, 13items
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Citation | Journal: Mol Cell / Year: 2023 Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses. Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / ...Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / Joseph D Puglisi / Oliver Mühlemann / Nenad Ban / Abstract: Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ...Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs. #1: Journal: Mol.Cell / Year: 2023 Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses Authors: Schubert, K. / Karousis, E.D. / Ban, I. / Lapointe, C.P. / Leibundgut, M. / Baeumlin, E. / Kummerant, E. / Scaiola, A. / Schoenhut, T. / Ziegelmueller, J. / Puglisi, J.D. / Muehlemann, O. / Ban, N. | ||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ppl.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ppl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ppl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ppl_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8ppl_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8ppl_validation.xml.gz | 256 KB | Display | |
Data in CIF | 8ppl_validation.cif.gz | 418.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/8ppl ftp://data.pdbj.org/pub/pdb/validation_reports/pp/8ppl | HTTPS FTP |
-Related structure data
Related structure data | 17805MC 8ppkC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Eukaryotic translation initiation factor ... , 15 types, 15 molecules I3I4I5I6I8IoIpIqIrIsItIuIvIxIy
#1: Protein | Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: Q9UBQ5 |
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#2: Protein | Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: O00303, ubiquitinyl hydrolase 1 |
#3: Protein | Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: Q9Y262 |
#4: Protein | Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: Q7L2H7 |
#5: Protein | Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: O15372 |
#6: Protein | Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: O75821 |
#7: Protein | Mass: 12752.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: N-terminus built as UNK / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P41567 |
#8: Protein | Mass: 16488.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P47813 |
#9: Protein | Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P05198 |
#10: Protein | Mass: 38454.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P20042 |
#11: Protein | Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P41091, protein-synthesizing GTPase |
#12: Protein | Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code Q14152 / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152 |
#13: Protein | Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P60228 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P60228 |
#15: Protein | Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code O15371 / Source: (natural) Homo sapiens (human) / References: UniProt: O15371 |
#16: Protein | Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: One linker built as UNK. UniProt accession code Q99613 Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: Q99613 |
-RNA chain , 2 types, 2 molecules IwA2
#14: RNA chain | Mass: 24463.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Aminoacylated initiator tRNA with base modifications. (XXX) refers to methionine residue attached to CCA-3'OH of tRNA. Sequence obtained from gtrnadb. Source: (natural) Homo sapiens (human) / Cell line: HEK293E |
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#17: RNA chain | Mass: 603609.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: unmodified sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU ...Details: unmodified sequence: >18S_rRNA_taoka_unmodified UACCUGGUUGAUCCUGCCAGUAGCAUaUGCUUGuCuCAAAGAUUAAGCCAUGCAUGUCUA AGUACGCACGGCCGGUACAGUGAAACUGCGAAuGGCUCaUUAAAuCAGuUAUGGUuCCuU uGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAaUUCUAGaGCUAAuAcAUGCCG ACGGGCGCUGACCCCCUUCGCGGGGGGGAuGCGUGCAuUUAUCAGAUCAAAACCAACCCG GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCuAGAU AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCuGCCCUA UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGuGACGGGGAAUCAGG GUUCGAUuCCGGAGAgGGAGCCUGAGAAACGGCUACCACAUcCAAGGaAGGCAGCAGGCG CGCaAAUUACCCACUCCCGACCCGGGGAgGUaGUGAcGAAAAAUAACAAUACAGGACUCU UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUuUAAaUCCUUUAACGAGGaUCCAUUGGAG gGCAAGUCuGGUGCCAGCAGcCGCGGuAAUUCCAGCUCCAAUAgCGUAuAuUAAAGUUGC UGCAGUUaAAAAGCUCGUAGuUgGAuCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU CCCGCGGGGCCCGAAGcGuUuACUUUGAAAAAAuuAGAGUGuUCAAAGCAGGCCCGAGCC GCCUGGAUACCGCAGCUAGGAAuAAugGAAUAGGACCGCGGUUCUAUUUUGUUGGUuUUC GGAACUGAGGCCAUGAUuAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU GAAAUuCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUuGCCAAGAAUGUUUUCA UUAAUCAAGAaCGAAAGUCGGAGGuuCGAAGACGAuCAGAUACCGUCGUAGUUCCGACCA uAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCuUCCG GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAuGGuUGCAAAGCUGAAACUUAAAGGAA UUGACGGAAGGGCACCACCAGGAGUGGAGCCuGCGGCuUAAUUuGACuCAACACGGGAAA CCUCACCCGGCcCGGACACGGACAGGAuUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG GGUGGuGgUGCAUGGCcGUUCUUAGUuGGUGGAGCGAUUUGUCUGGuUAAUUCCGAUAAC GAaCGAGACUcUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC UuCUuAgAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAgGUCUGUGAUG CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA UUAUuCCCCAUGAACGAGgAAUuCCCAGUAAGUGCGGGUCAUAAGCUuGCGUUGAUUaAG UCCCUGCCCUUuGUACACACCGcCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA ACUuGACUAUCUAGAGGAAGUAAAAGUCGUAaCAAGGUUUCcGUAGGUGaaCCUGCGGAA GGAUCAUUA Source: (natural) Homo sapiens (human) / Cell line: HEK293E |
+40S ribosomal protein ... , 28 types, 28 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARAUAVAWAXAYAZAaAbAcAd
-Small ribosomal subunit protein ... , 2 types, 2 molecules ASAT
#36: Protein | Mass: 17801.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: UniProt accession code P62269 S2: acetylserine (SAC) Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62269 |
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#37: Protein | Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: R67: omega-methylarginine (NMM) UniProt accession code P39019 Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P39019 |
-Protein , 4 types, 4 molecules AeAfAgAj
#48: Protein | Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P62861 (UniProt) NP_001988.1 (GeneBank) residues 1-74: ubiquitin Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62861 |
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#49: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: residues 1-76: ubiquitin zinc finger protein UniProt accession code P62979 Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62979 |
#50: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P63244 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P63244 |
#52: Protein | Mass: 24328.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 1-193 of MERS polyprotein ORF1ab UniProt accession number K9N7C7 (R1AB_MERS1) Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: rep, 1a-1b / Plasmid: pcDNA3.1(+) / Cell line (production host): HEK293E / Production host: Homo sapiens (human) / References: UniProt: K9N7C7 |
-Protein/peptide , 1 types, 1 molecules Ah
#51: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62945 / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P62945 |
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-Non-polymers , 6 types, 253 molecules
#53: Chemical | ChemComp-ZN / #54: Chemical | ChemComp-GTP / | #55: Chemical | ChemComp-MG / #56: Chemical | ChemComp-MET / | #57: Chemical | ChemComp-UNX / #58: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MERS-CoV Nsp1 - 43S pre-initiation complex / Type: RIBOSOME / Entity ID: #1-#13, #15-#52 / Source: NATURAL | ||||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: f.c. 100 nM | ||||||||||||||||
Specimen support | Details: 15 sec in easiGlow Discharge cleaning system (PELCO) at 15 mA Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8932 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3D reconstruction | Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218516 / Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: phenix.real_space_refine | |||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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