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- EMDB-8397: In situ structures of the genome and genome-delivery apparatus in... -

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Entry
Database: EMDB / ID: EMD-8397
TitleIn situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2
Map dataAsymmetric cryoEM reconstruction of Enterobacteria Phage MS2 at 3.6 Angstroms resolution.
Sample
  • Virus: Enterobacteria phage MS2 (virus)
    • Complex: capsid shell of Enterobacteria Phage MS2
      • Complex: coat protein of Enterobacteria Phage MS2
        • Protein or peptide: Capsid proteinCapsid
      • Complex: maturation protein of Enterobacteria Phage MS2
        • Protein or peptide: Maturation protein
    • Complex: the ssRNA genome of Enterobacteria Phage MS2
      • RNA: phage MS2 genome
Function / homology
Function and homology information


viral genome circularization / virion attachment to host cell pilus / negative regulation of viral translation / T=3 icosahedral viral capsid / virion component / regulation of translation / symbiont entry into host cell / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Assembly protein / Phage maturation protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Maturation protein A / Capsid protein
Similarity search - Component
Biological speciesEnterobacteria phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDai XH / Li ZH / Lai M / Shu S / Du YS / Zhou ZH / Sun R
CitationJournal: Nature / Year: 2017
Title: In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.
Authors: Xinghong Dai / Zhihai Li / Mason Lai / Sara Shu / Yushen Du / Z Hong Zhou / Ren Sun /
Abstract: Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump ...Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-coat protein interactions among 15 of these stem-loops with diverse sequences. The stem-loop at the 3' end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.
History
DepositionSep 17, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseDec 7, 2016-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
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  • Surface view colored by radius
  • Surface level: 3
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  • Surface view with fitted model
  • Atomic models: PDB-5tc1
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tc1
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5tc1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8397.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric cryoEM reconstruction of Enterobacteria Phage MS2 at 3.6 Angstroms resolution.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 3. / Movie #1: 3
Minimum - Maximum-7.5724845 - 13.481795
Average (Standard dev.)0.000000003076 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-7.57213.4820.000

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Supplemental data

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Additional map: Asymmetric cryoEM reconstruction of Enterobacteria Phage MS2 low-pass...

Fileemd_8397_additional.map
AnnotationAsymmetric cryoEM reconstruction of Enterobacteria Phage MS2 low-pass filtered to 6 Angstroms resolution to visualize the ssRNA genome.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Enterobacteria phage MS2

EntireName: Enterobacteria phage MS2 (virus)
Components
  • Virus: Enterobacteria phage MS2 (virus)
    • Complex: capsid shell of Enterobacteria Phage MS2
      • Complex: coat protein of Enterobacteria Phage MS2
        • Protein or peptide: Capsid proteinCapsid
      • Complex: maturation protein of Enterobacteria Phage MS2
        • Protein or peptide: Maturation protein
    • Complex: the ssRNA genome of Enterobacteria Phage MS2
      • RNA: phage MS2 genome

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Supramolecule #1: Enterobacteria phage MS2

SupramoleculeName: Enterobacteria phage MS2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The viral stock was obtained from ATCC (ATCC number 15597-B1) and cultured in Escherichia coli strain C-3000 (ATCC 15597).
NCBI-ID: 329852 / Sci species name: Enterobacteria phage MS2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: C-3000
Molecular weightTheoretical: 3.6 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 270.0 Å / T number (triangulation number): 3

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Supramolecule #2: capsid shell of Enterobacteria Phage MS2

SupramoleculeName: capsid shell of Enterobacteria Phage MS2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: The capsid of MS2 is composed of 178 copies of the coat protein and one single copy of the maturation protein.
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #3: coat protein of Enterobacteria Phage MS2

SupramoleculeName: coat protein of Enterobacteria Phage MS2 / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1
Details: The 178 copies of the coat protein are organized as 89 dimers in a T=3 icosahedral lattice.
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 14 KDa

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Supramolecule #4: maturation protein of Enterobacteria Phage MS2

SupramoleculeName: maturation protein of Enterobacteria Phage MS2 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2
Details: The single copy of maturation protein in the capsid shell of MS2 is located at one of the 2-fold symmetry axes and it replaces a coat protein dimer at this position.
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 44 KDa

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Supramolecule #5: the ssRNA genome of Enterobacteria Phage MS2

SupramoleculeName: the ssRNA genome of Enterobacteria Phage MS2 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3
Details: The genome of MS2 is a single-stranded RNA with 3569 bases. Our asymmetric cryoEM reconstruction of the MS2 virion shows that its ssRNA genome is well organized and has multiple contacts ...Details: The genome of MS2 is a single-stranded RNA with 3569 bases. Our asymmetric cryoEM reconstruction of the MS2 virion shows that its ssRNA genome is well organized and has multiple contacts with the capsid shell via tens of RNA stem-loop structures.
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1
Details: The capsid of MS2 contains 178 copies of the coat protein arranged as 89 dimers in a T=3 icosahedral lattice. Structure of the capsid has been solved by crystallography with icosahedral ...Details: The capsid of MS2 contains 178 copies of the coat protein arranged as 89 dimers in a T=3 icosahedral lattice. Structure of the capsid has been solved by crystallography with icosahedral symmetry applied (PDB ID 2MS2, also included as chains A, B, C in this model). Chains D, E, F, G, H are coat proteins that have slightly different structures in the asymmetric cryoEM reconstruction compared to the crystallographic structure. Structures of the other 170 copies of the coat protein are the same with 2MS2, and thus are not included due to the limited number of chain IDs.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 13.869659 KDa
SequenceString:
MASNFTQFVL VDNGGTGDVT VAPSNFANGV AEWISSNSRS QAYKVTCSVR QSSAQNRKYT IKVEVPKVAT QTVGGVELPV AAWRSYLNM ELTIPIFATN SDCELIVKAM QGLLKDGNPI PSAIAANSGI Y

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Macromolecule #2: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 2
Details: The capsid of MS2 contains a single copy of the maturation protein. Our structure shows that it replaces a coat protein dimer at one of the 2-fold icosahedral symmetry axes. Function of the ...Details: The capsid of MS2 contains a single copy of the maturation protein. Our structure shows that it replaces a coat protein dimer at one of the 2-fold icosahedral symmetry axes. Function of the maturation protein is to attach the MS2 virion to the host (E. coli) F-pili and deliver the ssRNA viral genome into the host during infection. of the icosahedral capsid. 178 copies of the coat protein arranged as 89 dimers in a T=3 icosahedral lattice. Structure of the capsid has been solved by crystallography with icosahedral symmetry applied (PDB ID 2MS2, also included as chains A, B, C in this model). Chains D, E, F, G, H are coat proteins that have slightly different structures in the asymmetric cryoEM reconstruction compared to the crystallographic structure. Structures of the other 170 copies of the coat protein are the same with 2MS2, and thus are not included due to the limited number of chain IDs.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 44.030934 KDa
SequenceString: MRAFSTLDRE NETFVPSVRV YADGETEDNS FSLKYRSNWT PGRFNSTGAK TKQWHYPSPY SRGALSVTSI DQGAYKRSGS SWGRPYEEK AGFGFSLDAR SCYSLFPVSQ NLTYIEVPQN VANRASTEVL QKVTQGNFNL GVALAEARST ASQLATQTIA L VKAYTAAR ...String:
MRAFSTLDRE NETFVPSVRV YADGETEDNS FSLKYRSNWT PGRFNSTGAK TKQWHYPSPY SRGALSVTSI DQGAYKRSGS SWGRPYEEK AGFGFSLDAR SCYSLFPVSQ NLTYIEVPQN VANRASTEVL QKVTQGNFNL GVALAEARST ASQLATQTIA L VKAYTAAR RGNWRQALRY LALNEDRKFR SKHVAGRWLE LQFGWLPLMS DIQGAYEMLT KVHLQEFLPM RAVRQVGTNI KL DGRLSYP AANFQTTCNI SRRIVIWFYI NDARLAWLSS LGILNPLGIV WEKVPFSFVV DWLLPVGNML EGLTAPVGCS YMS GTVTDV ITGESIISVD APYGWTVERQ GTAKAQISAM HRGVQSVWPT TGAYVKSPFS MVHTLDALAL IRQRLSR

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Macromolecule #3: phage MS2 genome

MacromoleculeName: phage MS2 genome / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 1.14720075 MDa
SequenceString: GGGUGGGACC CCUUUCGGGG UCCUGCUCAA CUUCCUGUCG AGCUAAUGCC AUUUUUAAUG UCUUUAGCGA GACGCUACCA UGGCUAUCG CUGUAGGUAG CCGGAAUUCC AUUCCUAGGA GGUUUGACCU GUGCGAGCUU UUAGUACCCU UGAUAGGGAG A ACGAGACC ...String:
GGGUGGGACC CCUUUCGGGG UCCUGCUCAA CUUCCUGUCG AGCUAAUGCC AUUUUUAAUG UCUUUAGCGA GACGCUACCA UGGCUAUCG CUGUAGGUAG CCGGAAUUCC AUUCCUAGGA GGUUUGACCU GUGCGAGCUU UUAGUACCCU UGAUAGGGAG A ACGAGACC UUCGUCCCCU CCGUUCGCGU UUACGCGGAC GGUGAGACUG AAGAUAACUC AUUCUCUUUA AAAUAUCGUU CG AACUGGA CUCCCGGUCG UUUUAACUCG ACUGGGGCCA AAACGAAACA GUGGCACUAC CCCUCUCCGU AUUCACGGGG GGC GUUAAG UGUCACAUCG AUAGAUCAAG GUGCCUACAA GCGAAGUGGG UCAUCGUGGG GUCGCCCGUA CGAGGAGAAA GCCG GUUUC GGCUUCUCCC UCGACGCACG CUCCUGCUAC AGCCUCUUCC CUGUAAGCCA AAACUUGACU UACAUCGAAG UGCCG CAGA ACGUUGCGAA CCGGGCGUCG ACCGAAGUCC UGCAAAAGGU CACCCAGGGU AAUUUUAACC UUGGUGUUGC UUUAGC AGA GGCCAGGUCG ACAGCCUCAC AACUCGCGAC GCAAACCAUU GCGCUCGUGA AGGCGUACAC UGCCGCUCGU CGCGGUA AU UGGCGCCAGG CGCUCCGCUA CCUUGCCCUA AACGAAGAUC GAAAGUUUCG AUCAAAACAC GUGGCCGGCA GGUGGUUG G AGUUGCAGUU CGGUUGGUUA CCACUAAUGA GUGAUAUCCA GGGUGCAUAU GAGAUGCUUA CGAAGGUUCA CCUUCAAGA GUUUCUUCCU AUGAGAGCCG UACGUCAGGU CGGUACUAAC AUCAAGUUAG AUGGCCGUCU GUCGUAUCCA GCUGCAAACU UCCAGACAA CGUGCAACAU AUCGCGACGU AUCGUGAUAU GGUUUUACAU AAACGAUGCA CGUUUGGCAU GGUUGUCGUC U CUAGGUAU CUUGAACCCA CUAGGUAUAG UGUGGGAAAA GGUGCCUUUC UCAUUCGUUG UCGACUGGCU CCUACCUGUA GG UAACAUG CUCGAGGGCC UUACGGCCCC CGUGGGAUGC UCCUACAUGU CAGGAACAGU UACUGACGUA AUAACGGGUG AGU CCAUCA UAAGCGUUGA CGCUCCCUAC GGGUGGACUG UGGAGAGACA GGGCACUGCU AAGGCCCAAA UCUCAGCCAU GCAU CGAGG GGUACAAUCC GUAUGGCCAA CAACUGGCGC GUACGUAAAG UCUCCUUUCU CGAUGGUCCA UACCUUAGAU GCGUU AGCA UUAAUCAGGC AACGGCUCUC UAGAUAGAGC CCUCAACCGG AGUUUGAAGC AUGGCUUCUA ACUUUACUCA GUUCGU UCU CGUCGACAAU GGCGGAACUG GCGACGUGAC UGUCGCCCCA AGCAACUUCG CUAACGGGGU CGCUGAAUGG AUCAGCU CU AACUCGCGUU CACAGGCUUA CAAAGUAACC UGUAGCGUUC GUCAGAGCUC UGCGCAGAAU CGCAAAUACA CCAUCAAA G UCGAGGUGCC UAAAGUGGCA ACCCAGACUG UUGGUGGUGU AGAGCUUCCU GUAGCCGCAU GGCGUUCGUA CUUAAAUAU GGAACUAACC AUUCCAAUUU UCGCUACGAA UUCCGACUGC GAGCUUAUUG UUAAGGCAAU GCAAGGUCUC CUAAAAGAUG GAAACCCGA UUCCCUCAGC AAUCGCAGCA AACUCCGGCA UCUACUAAUA GACGCCGGCC AUUCAAACAU GAGGAUUACC C AUGUCGAA GACAACAAAG AAGUUCAACU CUUUAUGUAU UGAUCUUCCU CGCGAUCUUU CUCUCGAAAU UUACCAAUCA AU UGCUUCU GUCGCUACUG GAAGCGGUGA UCCGCACAGU GACGACUUUA CAGCAAUUGC UUACUUAAGG GACGAAUUGC UCA CAAAGC AUCCGACCUU AGGUUCUGGU AAUGACGAGG CGACCCGUCG UACCUUAGCU AUCGCUAAGC UACGGGAGGC GAAU GGUGA UCGCGGUCAG AUAAAUAGAG AAGGUUUCUU ACAUGACAAA UCCUUGUCAU GGGAUCCGGA UGUUUUACAA ACCAG CAUC CGUAGCCUUA UUGGCAACCU CCUCUCUGGC UACCGAUCGU CGUUGUUUGG GCAAUGCACG UUCUCCAACG GUGCUC CUA UGGGGCACAA GUUGCAGGAU GCAGCGCCUU ACAAGAAGUU CGCUGAACAA GCAACCGUUA CCCCCCGCGC UCUGAGA GC GGCUCUAUUG GUCCGAGACC AAUGUGCGCC GUGGAUCAGA CACGCGGUCC GCUAUAACGA GUCAUAUGAA UUUAGGCU C GUUGUAGGGA ACGGAGUGUU UACAGUUCCG AAGAAUAAUA AAAUAGAUCG GGCUGCCUGU AAGGAGCCUG AUAUGAAUA UGUACCUCCA GAAAGGGGUC GGUGCUUUCA UCAGACGCCG GCUCAAAUCC GUUGGUAUAG ACCUGAAUGA UCAAUCGAUC AACCAGCGU CUGGCUCAGC AGGGCAGCGU AGAUGGUUCG CUUGCGACGA UAGACUUAUC GUCUGCAUCC GAUUCCAUCU C CGAUCGCC UGGUGUGGAG UUUUCUCCCA CCAGAGCUAU AUUCAUAUCU CGAUCGUAUC CGCUCACACU ACGGAAUCGU AG AUGGCGA GACGAUACGA UGGGAACUAU UUUCCACAAU GGGAAAUGGG UUCACAUUUG AGCUAGAGUC CAUGAUAUUC UGG GCAAUA GUCAAAGCGA CCCAAAUCCA UUUUGGUAAC GCCGGAACCA UAGGCAUCUA CGGGGACGAU AUUAUAUGUC CCAG UGAGA UUGCACCCCG UGUGCUAGAG GCACUUGCCU ACUACGGUUU UAAACCGAAU CUUCGUAAAA CGUUCGUGUC CGGGC UCUU UCGCGAGAGC UGCGGCGCGC ACUUUUACCG UGGUGUCGAU GUCAAACCGU UUUACAUCAA GAAACCUGUU GACAAU CUC UUCGCCCUGA UGCUGAUAUU AAAUCGGCUA CGGGGUUGGG GAGUUGUCGG AGGUAUGUCA GAUCCACGCC UCUAUAA GG UGUGGGUACG GCUCUCCUCC CAGGUGCCUU CGAUGUUCUU CGGUGGGACG GACCUCGCUG CCGACUACUA CGUAGUCA G CCCGCCUACG GCAGUCUCGG UAUACACCAA GACUCCGUAC GGGCGGCUGC UCGCGGAUAC CCGUACCUCG GGUUUCCGU CUUGCUCGUA UCGCUCGAGA ACGCAAGUUC UUCAGCGAAA AGCACGACAG UGGUCGCUAC AUAGCGUGGU UCCAUACUGG AGGUGAAAU CACCGACAGC AUGAAGUCCG CCGGCGUGCG CGUUAUACGC ACUUCGGAGU GGCUAACGCC GGUUCCCACA U UCCCUCAG GAGUGUGGGC CAGCGAGCUC UCCUCGGUAG CUGACCGAGG GACCCCCGUA AACGGGGUGG GUGUGCUCGA AA GAGCACG GGUGCGAAAG CGGUCCGGCU CCACCGAAAG GUGGGCGGGC UUCGGCCCAG GGACCUCCCC CUAAAGAGAG GAC CCGGGA UUCUCCCGAU UUGGUAACUA GCUGCUUGGC UAGUUACCAC CCA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: pH7.4 PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 20 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 79.0 K
DetailsEFTEM mode with Gatan GIF energy filter.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-14 / Number grids imaged: 2 / Number real images: 6080 / Average exposure time: 5.8 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 360000
CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: INSILICO MODEL
In silico model: A subset of particle images were processed with refine2d.py of EMAN1.9. The resulted 2D averages were processed with starticos of EMAN1.9 to produce an initial model with icosahedral ...In silico model: A subset of particle images were processed with refine2d.py of EMAN1.9. The resulted 2D averages were processed with starticos of EMAN1.9 to produce an initial model with icosahedral symmetry at roughly 50 Angstroms resolution.
Details: This initial model was used to do 3D classification of the dataset with C1 symmetry using Relion. One of the resulted 3D classes showed prominent genome densities was used as initial model ...Details: This initial model was used to do 3D classification of the dataset with C1 symmetry using Relion. One of the resulted 3D classes showed prominent genome densities was used as initial model for asymmetric structure refinement with Frealign.
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 5.0 degrees
Software - Name: FREALIGN (ver. 9.11) / Details: Frealign grid search (mode 3)
Final 3D classificationNumber classes: 10 / Avg.num./class: 30000 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11) / Details: Frealign local refinement (mode 1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 339718

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5tc1:
In situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2

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