[English] 日本語
Yorodumi
- EMDB-41037: Cryo-EM structure of immature Zika virus -

+
Open data


ID or keywords:

Loading...

-
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: Npj Viruses / Year: 2023
Title: Zika virus M protein latches and locks the E protein from transitioning to an immature state after prM cleavage.
Authors: Sydney A Majowicz / Anoop Narayanan / Ibrahim M Moustafa / Carol M Bator / Susan L Hafenstein / Joyce Jose /
Abstract: During flavivirus maturation, the structural proteins prM (pre-membrane) and E (envelope) undergo extensive low pH-mediated conformational changes, transitioning from spiky trimeric to smooth dimeric ...During flavivirus maturation, the structural proteins prM (pre-membrane) and E (envelope) undergo extensive low pH-mediated conformational changes, transitioning from spiky trimeric to smooth dimeric prM/E heterodimers which allow for furin cleavage of prM into pr and M and forms the irreversible mature conformation of smooth M/E heterodimers. The mechanisms of irreversible conformational changes to E protein following the pr cleavage are not understood. Utilizing cryo-EM structures of immature virus and structure-based mutagenesis of Zika virus, we identified two critical "latching and locking" interactions mediated by M protein residues Arg38 and Trp19, respectively, that stabilize the E protein structure in the smooth mature stage. M protein thus latches and locks the E protein in an irreversible mature structure, preventing premature fusion in the secretory pathway. Our studies provide mechanistic insights into the reversible structural transition of immature trimeric spikes and the irreversible transition of smooth dimeric M/E heterodimers critical for virus infectivity.
History
DepositionJun 9, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41037.png

Downloads & links

-
Map

FileDownload / File: emd_41037.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 400 pix.
= 880. Å		2.2 Å/pix.
x 400 pix.
= 880. Å		2.2 Å/pix.
x 400 pix.
= 880. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Mask #1

Fileemd_41037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
Entire : Zika virus

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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 94600
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

-
Atomic model buiding 1

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more