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- EMDB-41037: Cryo-EM structure of immature Zika virus -

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Basic information

Entry
Database: EMDB / ID: EMD-41037
TitleCryo-EM structure of immature Zika virus
Map datasharpened map
Sample
  • Virus: Zika virus
    • Protein or peptide: E-protein
    • Protein or peptide: prM-protein
KeywordsZika virus / immature / Cryo-EM / SPA / Homology modeling / prM cleavage / M protein / VIRUS
Biological speciesZika virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsMoustafa IM / Hafenstein SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)S10OD026822-01 United States
CitationJournal: Viruses / Year: 2023
Title: Zika virus M protein latches and locks the E protein from transitioning to an immature state after prM cleavage
Authors: Majowicz SA / Narayanan A / Moustafa IM / Bator CM / Hafenstein SL / Jose J
History
DepositionJun 9, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41037.png

Downloads & links

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Map

FileDownload / File: emd_41037.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.0237
Minimum - Maximum-0.04299267 - 0.12656198
Average (Standard dev.)-0.00011347428 (±0.011922923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 880.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-A map

Fileemd_41037_half_map_1.map
Annotationhalf-A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-B map

Fileemd_41037_half_map_2.map
Annotationhalf-B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zika virus

EntireName: Zika virus
Components
  • Virus: Zika virus
    • Protein or peptide: E-protein
    • Protein or peptide: prM-protein

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Supramolecule #1: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: prM/E protein / Diameter: 560.0 Å / T number (triangulation number): 3

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Macromolecule #1: E-protein

MacromoleculeName: E-protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
SequenceString: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQY VCKRTLVDRG WGNGCGLFGK GSLVTCAKFT CSKKMTGKSI QPENLEYRIM LSVHGSQHSG MIVNDTGYET DENRAKVEVT ...String:
IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQY VCKRTLVDRG WGNGCGLFGK GSLVTCAKFT CSKKMTGKSI QPENLEYRIM LSVHGSQHSG MIVNDTGYET DENRAKVEVT PNSPRAEATL GGFGSLGLDC EPRTGLDFSD LYYLTMNNKH WLVHKEWFHD IPLPWHAGAD TGTPHWNNKE ALVEFKDAHA KRQTVVVLGS QEGAVHTALA GALEAEMDGA KGKLFSGHLK CRLKMDKLRL KGVSYSLCTA AFTFTKVPAE TLHGTVTVEV QYAGTDGPCK IPVQMAVDMQ TLTPVGRLIT ANPVITESTE NSKMMLELDP PFGDSYIVIG VGDKKITHHW HRSGSTIGKA FEATVRGAKR MAVLGDTAWD FGSVGGVFNS LGKGIHQIFG AAFKSLFGGM SWFSQILIGT LLVWLGLNTK NGSISLTCLA LGGVMIFLST AVSA

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Macromolecule #2: prM-protein

MacromoleculeName: prM-protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
SequenceString:
AEITRRGSAY YMYLDRSDAG KAISFATTLG VNKCHVQIMD LGHMCDATMS YECPMLDEGV EPDDVDCWCN TTSTWVVYGT CHHKKGEARR SRRAVTLPSH STRKLQTRSQ TWLESREYTK HLIKVENWIF RNPGFALVAV AIAWLLGSST SQKVIYLVMI LLIAPAYS

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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

Concentration1.4 mg/mL
BufferpH: 7.4 / Details: TNE buffer
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K
Detailspurified immature zika virus at 1.4 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K
Specialist opticsSpherical aberration corrector: Microscope was modified with Cs corrector
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1839 / Average exposure time: 90.8 sec. / Average electron dose: 48.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.05 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 94600
Startup modelType of model: OTHER / Details: ab initio model
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 5696
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Modeller / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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