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- PDB-8ppl: MERS-CoV Nsp1 bound to the human 43S pre-initiation complex -

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Basic information

Entry
Database: PDB / ID: 8ppl
TitleMERS-CoV Nsp1 bound to the human 43S pre-initiation complex
Components
  • (40S ribosomal protein ...) x 28
  • (Eukaryotic translation initiation factor ...) x 15
  • (Small ribosomal subunit protein ...) x 2
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • Host translation inhibitor nsp1
  • Met-tRNAi(Met)
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
KeywordsTRANSLATION / 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 / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / positive regulation of mRNA cis splicing, via spliceosome / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e ...male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / positive regulation of mRNA cis splicing, via spliceosome / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / Response of EIF2AK1 (HRI) to heme deficiency / translation reinitiation / negative regulation of translational initiation in response to stress / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / : / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / PERK regulates gene expression / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation 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 / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / metal-dependent deubiquitinase activity / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / negative regulation of phagocytosis / NF-kappaB complex / rRNA modification in the nucleus and cytosol / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / pigmentation / protein kinase A binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / 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 / regulation of cell division / protein deubiquitination / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit binding / positive regulation of cyclic-nucleotide phosphodiesterase activity
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain ...Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / SUI1 domain / Non-structural protein 2, MERS-CoV-like / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / NSP3, SUD-C domain, MERS-CoV-like / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / AAA domain / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ubiquitin-like protein FUBI / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 40S ribosomal protein SA C-terminus / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / : / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S25 / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Replicase polyprotein 1ab / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D ...GUANOSINE-5'-TRIPHOSPHATE / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Replicase polyprotein 1ab / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Eukaryotic translation initiation factor 2 subunit 2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 1 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 1A, X-chromosomal / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsSchubert, 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
OrganizationGrant numberCountry
Swiss National Science Foundation182341 Switzerland
Swiss National Science Foundation182831 Switzerland
Swiss National Science Foundation204161 Switzerland
Swiss National Science Foundation51NF40-182880 Switzerland
Swiss National Science Foundation51NF40--205601 Switzerland
Other governmentETH-23 18-2 Switzerland
Other government Switzerland
Other private Switzerland
Other private Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM011378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145306 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG064690 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM144678 United States
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
DepositionJul 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I3: Eukaryotic translation initiation factor 3 subunit K
I4: Eukaryotic translation initiation factor 3 subunit F
I5: Eukaryotic translation initiation factor 3 subunit L
I6: Eukaryotic translation initiation factor 3 subunit M
I8: Eukaryotic translation initiation factor 3 subunit H
Io: Eukaryotic translation initiation factor 3 subunit G
Ip: Eukaryotic translation initiation factor 1
Iq: Eukaryotic translation initiation factor 1A, X-chromosomal
Ir: Eukaryotic translation initiation factor 2 subunit 1
Is: Eukaryotic translation initiation factor 2 subunit 2
It: Eukaryotic translation initiation factor 2 subunit 3
Iu: Eukaryotic translation initiation factor 3 subunit A
Iv: Eukaryotic translation initiation factor 3 subunit E
Iw: Met-tRNAi(Met)
Ix: Eukaryotic translation initiation factor 3 subunit D
Iy: Eukaryotic translation initiation factor 3 subunit C
A2: 18S rRNA
AA: 40S ribosomal protein SA
AB: 40S ribosomal protein S3a
AC: 40S ribosomal protein S2
AD: 40S ribosomal protein S3
AE: 40S ribosomal protein S4, X isoform
AF: 40S ribosomal protein S5
AG: 40S ribosomal protein S6
AH: 40S ribosomal protein S7
AI: 40S ribosomal protein S8
AJ: 40S ribosomal protein S9
AK: 40S ribosomal protein S10
AL: 40S ribosomal protein S11
AM: 40S ribosomal protein S12
AN: 40S ribosomal protein S13
AO: 40S ribosomal protein S14
AP: 40S ribosomal protein S15
AQ: 40S ribosomal protein S16
AR: 40S ribosomal protein S17
AS: Small ribosomal subunit protein uS13
AT: Small ribosomal subunit protein eS19
AU: 40S ribosomal protein S20
AV: 40S ribosomal protein S21
AW: 40S ribosomal protein S15a
AX: 40S ribosomal protein S23
AY: 40S ribosomal protein S24
AZ: 40S ribosomal protein S25
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
Ac: 40S ribosomal protein S28
Ad: 40S ribosomal protein S29
Ae: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Af: Ubiquitin-40S ribosomal protein S27a
Ag: Receptor of activated protein C kinase 1
Ah: 60S ribosomal protein L41
Aj: Host translation inhibitor nsp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,078,202303
Polymers2,074,44852
Non-polymers3,753251
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Eukaryotic translation initiation factor ... , 15 types, 15 molecules I3I4I5I6I8IoIpIqIrIsItIuIvIxIy

#1: Protein Eukaryotic translation initiation factor 3 subunit K / Eukaryotic initiation factor 3 / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


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
#2: Protein Eukaryotic translation initiation factor 3 subunit F / Eukaryotic initiation factor 3 / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


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 Eukaryotic translation initiation factor 3 subunit L / Eukaryotic initiation factor 3 / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting 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 Eukaryotic translation initiation factor 3 subunit M / Eukaryotic initiation factor 3 / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


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 Eukaryotic translation initiation factor 3 subunit H / Eukaryotic initiation factor 3 / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


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 Eukaryotic translation initiation factor 3 subunit G / Eukaryotic initiation factor 3 / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


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 Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


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 Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


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 Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


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 Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


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 Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


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 Eukaryotic translation initiation factor 3 subunit A / Eukaryotic initiation factor 3 / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


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 Eukaryotic translation initiation factor 3 subunit E / Eukaryotic initiation factor 3 / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


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 Eukaryotic translation initiation factor 3 subunit D / Eukaryotic initiation factor 3 / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


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 Eukaryotic translation initiation factor 3 subunit C / Eukaryotic initiation factor 3 / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


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

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RNA chain , 2 types, 2 molecules IwA2

#14: RNA chain Met-tRNAi(Met)


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
#17: RNA chain 18S rRNA / 18S ribosomal RNA


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

#18: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32925.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: UniProt accession code P08865 S2: acetylserine (SAC)
Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P08865
#19: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P61247 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P61247
#20: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P15880 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P15880
#21: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P23396 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#22: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62701 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62701
#23: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P46782 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P46782
#24: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62753 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62753
#25: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62081 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62081
#26: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Uniprot accession code P62241 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62241
#27: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P46781 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P46781
#28: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P46783 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P46783
#29: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62280 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62280
#30: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P25398 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P25398
#31: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62277 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62277
#32: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: D138: isoaspartate (IAS) UniProt accession code P62263
Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62263
#33: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62841 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62841
#34: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P62249 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62249
#35: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P08708 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P08708
#38: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P60866 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P60866
#39: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9166.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: UniProt accession code P63220 M1: acetylmethionine (AME)
Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P63220
#40: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62244 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62244
#41: Protein 40S ribosomal protein S23 /


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: UniProt accession code P62266 P62: hydroxyproline (HY3)
Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: A0A4W2DI10
#42: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62847 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62847
#43: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62851 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62851
#44: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62854 zinc finger protein / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62854
#45: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P42677 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P42677
#46: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62857 / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62857
#47: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt accession code P62273 zinc finger protein / Source: (natural) Homo sapiens (human) / Cell line: HEK293E / References: UniProt: P62273

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Small ribosomal subunit protein ... , 2 types, 2 molecules ASAT

#36: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18 / Ke-3 / Ke3


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
#37: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


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

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Protein , 4 types, 4 molecules AeAfAgAj

#48: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin like and ribosomal protein S30 fusion


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
#49: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


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 Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


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 Host translation inhibitor nsp1 / nsp1 / Leader 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

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Protein/peptide , 1 types, 1 molecules Ah

#51: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#54: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 116 / Source method: obtained synthetically / Formula: Mg
#56: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11NO2S
#57: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 129 / Source method: obtained synthetically
#58: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: MERS-CoV Nsp1 - 43S pre-initiation complex / Type: RIBOSOME / Entity ID: #1-#13, #15-#52 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES-KOH1
2100 mMKOAc1
310 mMMg(OAc)21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: f.c. 100 nM
Specimen supportDetails: 15 sec in easiGlow Discharge cleaning system (PELCO) at 15 mA
Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8932

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Processing

EM software
IDNameVersionCategoryDetails
7Coot0.9.8.5model fitting
9PHENIX1.20.1model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218516 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: phenix.real_space_refine
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
16ZOK

6zok

6ZOK40S body1
26ZOL

6zol

6ZOL40S head2

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