[English] 日本語
Yorodumi
- EMDB-29300: Mojiang virus F ectodomain in prefusion form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29300
TitleMojiang virus F ectodomain in prefusion form
Map data
Sample
  • Complex: Mojiang virus F glycoprotein ectodomain in the prefusion form
    • Protein or peptide: Fusion glycoprotein F0
KeywordsF ectodomain / prefusion / VIRAL PROTEIN
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMojiang virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsLow YS / Isaacs A / Modhiran N / Watterson D
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GA82108 Australia
CitationJournal: Nat Commun / Year: 2023
Title: Structure and antigenicity of divergent Henipavirus fusion glycoproteins.
Authors: Ariel Isaacs / Yu Shang Low / Kyle L Macauslane / Joy Seitanidou / Cassandra L Pegg / Stacey T M Cheung / Benjamin Liang / Connor A P Scott / Michael J Landsberg / Benjamin L Schulz / Keith ...Authors: Ariel Isaacs / Yu Shang Low / Kyle L Macauslane / Joy Seitanidou / Cassandra L Pegg / Stacey T M Cheung / Benjamin Liang / Connor A P Scott / Michael J Landsberg / Benjamin L Schulz / Keith J Chappell / Naphak Modhiran / Daniel Watterson /
Abstract: In August 2022, a novel henipavirus (HNV) named Langya virus (LayV) was isolated from patients with severe pneumonic disease in China. This virus is closely related to Mòjiāng virus (MojV), and ...In August 2022, a novel henipavirus (HNV) named Langya virus (LayV) was isolated from patients with severe pneumonic disease in China. This virus is closely related to Mòjiāng virus (MojV), and both are divergent from the bat-borne HNV members, Nipah (NiV) and Hendra (HeV) viruses. The spillover of LayV is the first instance of a HNV zoonosis to humans outside of NiV and HeV, highlighting the continuing threat this genus poses to human health. In this work, we determine the prefusion structures of MojV and LayV F proteins via cryogenic electron microscopy to 2.66 and 3.37 Å, respectively. We show that despite sequence divergence from NiV, the F proteins adopt an overall similar structure but are antigenically distinct as they do not react to known antibodies or sera. Glycoproteomic analysis revealed that while LayV F is less glycosylated than NiV F, it contains a glycan that shields a site of vulnerability previously identified for NiV. These findings explain the distinct antigenic profile of LayV and MojV F, despite the extent to which they are otherwise structurally similar to NiV. Our results carry implications for broad-spectrum HNV vaccines and therapeutics, and indicate an antigenic, yet not structural, divergence from prototypical HNVs.
History
DepositionDec 26, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29300.png

Downloads & links

-
Map

FileDownload / File: emd_29300.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.21351932 - 0.47196475
Average (Standard dev.)0.0008025257 (±0.014833559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_29300_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_29300_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_29300_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29300_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mojiang virus F glycoprotein ectodomain in the prefusion form

EntireName: Mojiang virus F glycoprotein ectodomain in the prefusion form
Components
  • Complex: Mojiang virus F glycoprotein ectodomain in the prefusion form
    • Protein or peptide: Fusion glycoprotein F0

-
Supramolecule #1: Mojiang virus F glycoprotein ectodomain in the prefusion form

SupramoleculeName: Mojiang virus F glycoprotein ectodomain in the prefusion form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mojiang virus
Molecular weightTheoretical: 200 KDa

-
Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mojiang virus
Molecular weightTheoretical: 52.636922 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MALNKNMFSS LFLGYLLVYA TTVQSSIHYD SLSKVGVIKG LTYNYKIKGS PSTKLMVVKL IPNIDSVKNC TQKQYDEYKN LVRKALEPV KMAIDTMLNN VKSGNNKYRF AGAIMAGVAL GVATAATVTA GIALHRSNEN AQAIANMKSA IQNTNEAVKQ L QLANKQTL ...String:
MALNKNMFSS LFLGYLLVYA TTVQSSIHYD SLSKVGVIKG LTYNYKIKGS PSTKLMVVKL IPNIDSVKNC TQKQYDEYKN LVRKALEPV KMAIDTMLNN VKSGNNKYRF AGAIMAGVAL GVATAATVTA GIALHRSNEN AQAIANMKSA IQNTNEAVKQ L QLANKQTL AVIDTIRGEI NNNIIPVINQ LSCDTIGLSV GIRLTQYYSE IITAFGPALQ NPVNTRITIQ AISSVFNGNF DE LLKIMGY TSGDLYEILH SELIRGNIID VDVDAGYIAL EIEFPNLTLV PNAVVQELMP ISYNIDGDEW VTLVPRFVLT RTT LLSNID TSRCTITDSS VICDNDYALP MSHELIGCLQ GDTSKCAREK VVSSYVPKFA LSDGLVYANC LNTICRCMDT DTPI SQSLG ATVSLLDNKR CSVYQVGDVL ISVGSYLGDG EYNADNVELG PPIVIDKIDI GNQLAGINQT LQEAEDYIEK SEEFL KG

UniProtKB: Fusion glycoprotein F0

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 6.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
Details0.255% CHAPS added

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 2543223
Startup modelType of model: OTHER
Details: Ad initio reconstruction, maximum likelihood method
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 213754
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 87232 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 102.7
Output model

PDB-8fmy:
Mojiang virus F ectodomain in prefusion form

+
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