Cryo-EM reconstruction of the bacteriophage T4 isometric capsid

2024-03-13 REL RCSB RCSB RCSB 2017-04-06 2017-07-19 2017-09-13 2024-03-13 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI081726 United States National Institutes of Health/Office of the Director S10 OD012372 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P01 GM098412-S1 United States Cryo-EM reconstruction of the bacteriophage T4 isometric capsid Chen Z Sun L Bacteriophage T4, isometric head, virus capsid assembly, triangulation numbers, size-determining mutations, capsid stabilization, capsid decoration proteins, VIRUS Chen Z Sun L Zhang Z Fokine A Padilla-Sanchez V Hanein D Jiang W Rossmann MG Rao VB Cryo-EM structure of the bacteriophage T4 isometric head at 3.3- angstrom resolution and its relevance to the assembly of icosahedral viruses. Proc. Natl. Acad. Sci. U.S.A. US 114 E8184 E8193 2017 28893988 doi:10.1073/pnas.1708483114 1091-6490 0040 PNASA6 5vf3 FULLOVERLAP Enterobacteria phage T4 Enterobacteria phage T4 0 1 2 3 4 5 Enterobacteria phage T4 Escherichia coli gp23*-gp24*-Soc-Hoc 860.0 13 VIRION SPECIES false true Capsid vertex protein gp24 Enterobacteria phage T4 0.045838574 1 LEVO STTTNSNSIGRPNLVALTRATTKLIYSDIVATQRTNQPVAAFYGIKYLNPDNEFTFKTGATYAGEAGYVDREQITELTEE SKLTLNKGDLFKYNNIVYKVLEDTPFATIEESDLELALQIAIVLLKVRLFSDAASTSKFESSDSEIADARFQINKWQTAV KSRKLKTGITVELAQDLEANGFDAPNFLEDLLATEMADEINKDILQSLITVSKRYKVTGITDSGFIDLSYASAPEAGRSL YRMVCEMVSHIQKESTYTATFCVASARAAAILAASGWLKHKPEDDKYLSQNAYGFLANGLPLYCDTNSPLDYVIVGVVEN IGEKEIVGSIFYAPYTEGLDLDDPEHVGAFKVVVDPESLQPSIGLLVRYALSANPYTVAKDEKEARIIDGGDMDKMAGRS DLSVLLGVKLPKIIIDE P19896 Major capsid protein Enterobacteria phage T4 0.048728863 12 LEVO AEIGGDHGYNATNIAAGQTSGAVTQIGPAVMGMVRRAIPNLIAFDICGVQPMNSPTGQVFALRAVYGKDPVAAGAKEAFH PMYGPDAMFSGQGAAKKFPALAASTQTTVGDIYTHFFQETGTVYLQASVQVTIDAGATDAAKLDAEIKKQMEAGALVEIA EGMATSIAELQEGFNGSTDNPWNEMGFRIDKQVIEAKSRQLKAAYSIELTQDLRAVHGMDADAELSGILATEIMLEINRE VVDWINYSAQVGKSGMTLTPGSKAGVFDFQDPIDIRGARWAGESFKALLFQIDKEAVEIARQTGRGEGNFIIASRNVVNV LASVDTGISYAAQGLATGFSTDTTKSVFAGVLGGKYRVYIDQYAKQDYFTVGYKGPNEMDAGIYYAPYVALTPLRGSDPK NFQPVMGFKTRYGIGINPFAESAAQAPASRIQSGMPSILNSLGKNAYFRRVYVKGI P04535 Small outer capsid protein Enterobacteria phage T4 0.009085095 11 LEVO MASARGYVNIKTFEQKLDGNKKIEGKEVSVAFPLYSDVHKISGAHYQTFPSEKAAYSTVYEENQRTEWIAANEDLWKVTG P03715 Highly immunogenic outer capsid protein Enterobacteria phage T4 0.040416547 1 LEVO MTFTVDITPKTPTGVIDETKQFTATPSGQTGGGTITYAWSVDNVPQDGAEATFSYVLKGPAGQKTIKVVATNTLSEGGPE TAEATTTITVKNKTQTTTLAVTPASPAAGVIGTPVQFTAALASQPDGASATYQWYVDDSQVGGETNSTFSYTPTTSGVKR IKCVAQVTATDYDALSVTSNEVSLTVNKKTMNPQVTLTPPSINVQQDASATFTANVTGAPEEAQITYSWKKDSSPVEGST NVYTVDTSSVGSQTIEVTATVTAADYNPVTVTKTGNVTVTAKVAPEPEGELPYVHPLPHRSSAYIWCGWWVMDEIQKMTE EGKDWKTDDPDSKYYLHRYTLQKMMKDYPEVDVQESRNGYIIHKTALETGIIYTYP P18056 Highly immunogenic outer capsid protein Enterobacteria phage T4 0.001294587 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) singleParticle twoDArray 1 7.0

50 mM sodium phosphate, pH 7.0, 75 mM sodium chloride, 1 mM magnesium chloride

Ted Pella COPPER 400 CARBON LACEY 3.0 GLOW DISCHARGE 60 AIR 0.04

glow discharge for 60 seconds with 30 mA current

ETHANE 80 298 GATAN CRYOPLUNGE 3

Blot for 8 seconds before plunging..

High-purity sample, volume = 50 uL, 10^12 particles

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 -1.0 -0.8 -3.0 -3.5 18000.0 18000.0 OTHER NITROGEN 90.0 100.0 0.5

Data collection by Leginon

GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3710 3838 3-22 1 3000 9.0 26.0

Images were collected in super-resolution mode at 40 frames per second.

The selected images were gain-normalized.

19000

Approximately 1000 manually-picked particles were used for 2D classification. Templates were then generated from these 2D classes and used for automated particle picking.

EMAN was used to generate an initial model from about 1000 randomly-oriented particles.

60 I FOURIER SPACE 3.3 FSC 0.143 CUT-OFF

Independent refinement of even/odd map, gold standard

18000 COMMON LINE

Randomly assigned for the particles used for initial model

COMMON LINE EMAN, JSPR

EMAN and JSPR were used for refinement.

200 15.0 RELION

Relion was used for reference-free 2D classification.

emd_8661.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1536 1536 1536 -768 -768 -768 1536 1536 1536 1244.16 1244.16 1244.16 90.0 90.0 90.0 X Y Z -31.032540000000001 42.346490000000003 0.005835759 1.7083335 0.81 0.81 0.81 8.0 EMDB ::::EMDATABANK.org::::EMD-8661:::: Cryo-EM reconstruction of the bacteriophage T4 isometric capsid AB INITIO MODEL REAL