Cryo-EM structure of thermally stable Zika virus strain H/PF/2013

2024-10-23 REL PDBj RCSB PDBj 2016-05-09 2016-05-25 2016-05-25 2024-10-23 Ministry of Education MOE2012-T3-1-008 Singapore National Research Foundation NRF-NRFI2016-01 Singapore Ministry of Health Duke-NUS Signature Research Program Singapore Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 Kostyuchenko VA Zhang S Fibriansah G Lok SM viral protein, flavivirus, glycoprotein, zika virus, VIRUS Kostyuchenko VA Lim EX Zhang S Fibriansah G Ng TS Ooi JS Shi J Lok SM Structure of the thermally stable Zika virus Nature UK 533 425 428 2016 27093288 doi:10.1038/nature17994 1476-4687 0006 NATUAS 5iz7 FULLOVERLAP Zika virus Zika virus 0 1 2 Zika virus H/PF/2013 Homo sapiens 10 glycoprotein shell 480.0 1 VIRION STRAIN true false structural protein E Zika virus H/PF/2013 0.054444051

glycosylated at N154

3 LEVO IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEA YLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAE TLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHW HRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK NGSISLMCLALGGVLIFLSTAVSA A0A024B7W1 structural protein M Zika virus H/PF/2013 0.008496883 3 LEVO AVTLPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKVIYLVMILLIAPAYS A0A0U4DG08 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 8.0 10.0 C4H12ClNO3 Tris-HCl 120.0 NaCl Sodium Chloride 1.0 C10H16N2O8 EDTA Quantifoil COPPER 400 CARBON LACEY CARBON CONTINUOUS GLOW DISCHARGE ETHANE 100 298 FEI VITROBOT MARK IV

blot for 1s.

purified with PEG precipitation, sucrose cushion and potassium tartrate gradient

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 FEI FALCON II (4k x 4k) OTHER 4096 4096 2-11 1 3086 1.8 50.0 1

images collected in movie mode, 30 frames per 1.8s exposure; frames aligned with MotionCorr, frames 2-11 averaged to produce images for further processing

11600

manually picked

EMD-2485 7180 I FOURIER SPACE 3.7 FSC 0.143 CUT-OFF EMAN 1.9 7180 PROJECTION MATCHING 20 0.1 EMAN 1.9 MPSA PROJECTION MATCHING 20 0.1 EMAN 1.9 MPSA 1 emd_8139.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 -200 -200 -200 400 400 400 536.0 536.0 536.0 90.0 90.0 90.0 X Y Z -6.233699 11.108053999999999 0.000000001451599 1.0 1.34 1.34 1.34 3.5 AUTHOR ::::EMDATABANK.org::::EMD-8139:::: None 3J27 A 1-495 PDB experimental model 3J27 B 1-72 PDB experimental model BACKBONE TRACE

Only icosahedral symmetry imposed. Rwork 0.323 Rtest 0.324

residual RECIPROCAL