2024-11-20 REL RCSB RCSB RCSB 2016-09-17 2016-12-07 2016-12-07 2024-11-20 Dai XH Li ZH asymmetric cryoEM reconstruction, ssRNA genome structure, genome-delivery apparatus, genome-capsid interactions, viral protein-rna complex Dai X Li Z Lai M Shu S Du Y Zhou ZH Sun R Nature UK 541 112 116 2017 27992877 doi:10.1038/nature20589 1476-4687 0006 NATUAS 5tc1 FULLOVERLAP Enterobacteria phage MS2 Enterobacteria phage MS2 0 1 2 3

The viral stock was obtained from ATCC (ATCC number 15597-B1) and cultured in Escherichia coli strain C-3000 (ATCC 15597).

Enterobacteria phage MS2 Escherichia coli C-3000 3.6 capsid 270.0 3 VIRION SPECIES false false capsid shell of Enterobacteria Phage MS2 1 1 2

The capsid of MS2 is composed of 178 copies of the coat protein and one single copy of the maturation protein.

Enterobacteria phage MS2 2.5 coat protein of Enterobacteria Phage MS2 2 1

The 178 copies of the coat protein are organized as 89 dimers in a T=3 icosahedral lattice.

Enterobacteria phage MS2 0.014 maturation protein of Enterobacteria Phage MS2 2 2

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.

Enterobacteria phage MS2 0.044 the ssRNA genome of Enterobacteria Phage MS2 1 3

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.

Enterobacteria phage MS2 1.1 Capsid protein Enterobacteria phage MS2 0.013869659

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.

8 LEVO MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVELPV AAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIY P03612 Maturation protein Enterobacteria phage MS2 0.044030934

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.

1 LEVO MRAFSTLDRENETFVPSVRVYADGETEDNSFSLKYRSNWTPGRFNSTGAKTKQWHYPSPYSRGALSVTSIDQGAYKRSGS SWGRPYEEKAGFGFSLDARSCYSLFPVSQNLTYIEVPQNVANRASTEVLQKVTQGNFNLGVALAEARSTASQLATQTIAL VKAYTAARRGNWRQALRYLALNEDRKFRSKHVAGRWLELQFGWLPLMSDIQGAYEMLTKVHLQEFLPMRAVRQVGTNIKL DGRLSYPAANFQTTCNISRRIVIWFYINDARLAWLSSLGILNPLGIVWEKVPFSFVVDWLLPVGNMLEGLTAPVGCSYMS GTVTDVITGESIISVDAPYGWTVERQGTAKAQISAMHRGVQSVWPTTGAYVKSPFSMVHTLDALALIRQRLSR P03610 phage MS2 genome Enterobacteria phage MS2 1.1472007499999999 1 GGGUGGGACCCCUUUCGGGGUCCUGCUCAACUUCCUGUCGAGCUAAUGCCAUUUUUAAUGUCUUUAGCGAGACGCUACCA UGGCUAUCGCUGUAGGUAGCCGGAAUUCCAUUCCUAGGAGGUUUGACCUGUGCGAGCUUUUAGUACCCUUGAUAGGGAGA ACGAGACCUUCGUCCCCUCCGUUCGCGUUUACGCGGACGGUGAGACUGAAGAUAACUCAUUCUCUUUAAAAUAUCGUUCG AACUGGACUCCCGGUCGUUUUAACUCGACUGGGGCCAAAACGAAACAGUGGCACUACCCCUCUCCGUAUUCACGGGGGGC GUUAAGUGUCACAUCGAUAGAUCAAGGUGCCUACAAGCGAAGUGGGUCAUCGUGGGGUCGCCCGUACGAGGAGAAAGCCG GUUUCGGCUUCUCCCUCGACGCACGCUCCUGCUACAGCCUCUUCCCUGUAAGCCAAAACUUGACUUACAUCGAAGUGCCG CAGAACGUUGCGAACCGGGCGUCGACCGAAGUCCUGCAAAAGGUCACCCAGGGUAAUUUUAACCUUGGUGUUGCUUUAGC AGAGGCCAGGUCGACAGCCUCACAACUCGCGACGCAAACCAUUGCGCUCGUGAAGGCGUACACUGCCGCUCGUCGCGGUA AUUGGCGCCAGGCGCUCCGCUACCUUGCCCUAAACGAAGAUCGAAAGUUUCGAUCAAAACACGUGGCCGGCAGGUGGUUG GAGUUGCAGUUCGGUUGGUUACCACUAAUGAGUGAUAUCCAGGGUGCAUAUGAGAUGCUUACGAAGGUUCACCUUCAAGA GUUUCUUCCUAUGAGAGCCGUACGUCAGGUCGGUACUAACAUCAAGUUAGAUGGCCGUCUGUCGUAUCCAGCUGCAAACU UCCAGACAACGUGCAACAUAUCGCGACGUAUCGUGAUAUGGUUUUACAUAAACGAUGCACGUUUGGCAUGGUUGUCGUCU CUAGGUAUCUUGAACCCACUAGGUAUAGUGUGGGAAAAGGUGCCUUUCUCAUUCGUUGUCGACUGGCUCCUACCUGUAGG UAACAUGCUCGAGGGCCUUACGGCCCCCGUGGGAUGCUCCUACAUGUCAGGAACAGUUACUGACGUAAUAACGGGUGAGU CCAUCAUAAGCGUUGACGCUCCCUACGGGUGGACUGUGGAGAGACAGGGCACUGCUAAGGCCCAAAUCUCAGCCAUGCAU CGAGGGGUACAAUCCGUAUGGCCAACAACUGGCGCGUACGUAAAGUCUCCUUUCUCGAUGGUCCAUACCUUAGAUGCGUU AGCAUUAAUCAGGCAACGGCUCUCUAGAUAGAGCCCUCAACCGGAGUUUGAAGCAUGGCUUCUAACUUUACUCAGUUCGU UCUCGUCGACAAUGGCGGAACUGGCGACGUGACUGUCGCCCCAAGCAACUUCGCUAACGGGGUCGCUGAAUGGAUCAGCU CUAACUCGCGUUCACAGGCUUACAAAGUAACCUGUAGCGUUCGUCAGAGCUCUGCGCAGAAUCGCAAAUACACCAUCAAA GUCGAGGUGCCUAAAGUGGCAACCCAGACUGUUGGUGGUGUAGAGCUUCCUGUAGCCGCAUGGCGUUCGUACUUAAAUAU GGAACUAACCAUUCCAAUUUUCGCUACGAAUUCCGACUGCGAGCUUAUUGUUAAGGCAAUGCAAGGUCUCCUAAAAGAUG GAAACCCGAUUCCCUCAGCAAUCGCAGCAAACUCCGGCAUCUACUAAUAGACGCCGGCCAUUCAAACAUGAGGAUUACCC AUGUCGAAGACAACAAAGAAGUUCAACUCUUUAUGUAUUGAUCUUCCUCGCGAUCUUUCUCUCGAAAUUUACCAAUCAAU UGCUUCUGUCGCUACUGGAAGCGGUGAUCCGCACAGUGACGACUUUACAGCAAUUGCUUACUUAAGGGACGAAUUGCUCA CAAAGCAUCCGACCUUAGGUUCUGGUAAUGACGAGGCGACCCGUCGUACCUUAGCUAUCGCUAAGCUACGGGAGGCGAAU GGUGAUCGCGGUCAGAUAAAUAGAGAAGGUUUCUUACAUGACAAAUCCUUGUCAUGGGAUCCGGAUGUUUUACAAACCAG CAUCCGUAGCCUUAUUGGCAACCUCCUCUCUGGCUACCGAUCGUCGUUGUUUGGGCAAUGCACGUUCUCCAACGGUGCUC CUAUGGGGCACAAGUUGCAGGAUGCAGCGCCUUACAAGAAGUUCGCUGAACAAGCAACCGUUACCCCCCGCGCUCUGAGA GCGGCUCUAUUGGUCCGAGACCAAUGUGCGCCGUGGAUCAGACACGCGGUCCGCUAUAACGAGUCAUAUGAAUUUAGGCU CGUUGUAGGGAACGGAGUGUUUACAGUUCCGAAGAAUAAUAAAAUAGAUCGGGCUGCCUGUAAGGAGCCUGAUAUGAAUA UGUACCUCCAGAAAGGGGUCGGUGCUUUCAUCAGACGCCGGCUCAAAUCCGUUGGUAUAGACCUGAAUGAUCAAUCGAUC AACCAGCGUCUGGCUCAGCAGGGCAGCGUAGAUGGUUCGCUUGCGACGAUAGACUUAUCGUCUGCAUCCGAUUCCAUCUC CGAUCGCCUGGUGUGGAGUUUUCUCCCACCAGAGCUAUAUUCAUAUCUCGAUCGUAUCCGCUCACACUACGGAAUCGUAG AUGGCGAGACGAUACGAUGGGAACUAUUUUCCACAAUGGGAAAUGGGUUCACAUUUGAGCUAGAGUCCAUGAUAUUCUGG GCAAUAGUCAAAGCGACCCAAAUCCAUUUUGGUAACGCCGGAACCAUAGGCAUCUACGGGGACGAUAUUAUAUGUCCCAG UGAGAUUGCACCCCGUGUGCUAGAGGCACUUGCCUACUACGGUUUUAAACCGAAUCUUCGUAAAACGUUCGUGUCCGGGC UCUUUCGCGAGAGCUGCGGCGCGCACUUUUACCGUGGUGUCGAUGUCAAACCGUUUUACAUCAAGAAACCUGUUGACAAU CUCUUCGCCCUGAUGCUGAUAUUAAAUCGGCUACGGGGUUGGGGAGUUGUCGGAGGUAUGUCAGAUCCACGCCUCUAUAA GGUGUGGGUACGGCUCUCCUCCCAGGUGCCUUCGAUGUUCUUCGGUGGGACGGACCUCGCUGCCGACUACUACGUAGUCA GCCCGCCUACGGCAGUCUCGGUAUACACCAAGACUCCGUACGGGCGGCUGCUCGCGGAUACCCGUACCUCGGGUUUCCGU CUUGCUCGUAUCGCUCGAGAACGCAAGUUCUUCAGCGAAAAGCACGACAGUGGUCGCUACAUAGCGUGGUUCCAUACUGG AGGUGAAAUCACCGACAGCAUGAAGUCCGCCGGCGUGCGCGUUAUACGCACUUCGGAGUGGCUAACGCCGGUUCCCACAU UCCCUCAGGAGUGUGGGCCAGCGAGCUCUCCUCGGUAGCUGACCGAGGGACCCCCGUAAACGGGGUGGGUGUGCUCGAAA GAGCACGGGUGCGAAAGCGGUCCGGCUCCACCGAAAGGUGGGCGGGCUUCGGCCCAGGGACCUCCCCCUAAAGAGAGGAC CCGGGAUUCUCCCGAUUUGGUAACUAGCUGCUUGGCUAGUUACCACCCA V00642.1 singleParticle particle 7.4

pH7.4 PBS

Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 30 OTHER ETHANE 100 295 FEI VITROBOT MARK II FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 130000.0 47170.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 79.0 GIF 20 20

EFTEM mode with Gatan GIF energy filter.

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 7676 7420 1-14 2 6080 5.8 50.0 1 360000 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.

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.

1 C1 FOURIER SPACE 3.6 FSC 0.143 CUT-OFF FREALIGN 9.11 339718 PROJECTION MATCHING 5.0 FREALIGN 9.11

Frealign grid search (mode 3)

PROJECTION MATCHING FREALIGN 9.11

Frealign local refinement (mode 1)

10 30000.0 RELION 1.4 AB INITIO MODEL REAL emd_8397_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 -160 -160 -160 320 320 320 339.19998 339.19998 339.19998 90.0 90.0 90.0 X Y Z -1.2095244 5.930885 -0.000000015831503 1.0 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::D_1000224002:::: Asymmetric cryoEM reconstruction of Enterobacteria Phage MS2 low-pass filtered to 6 Angstroms resolution to visualize the ssRNA genome.