[English] 日本語
Yorodumi
- EMDB-29029: Langya Virus Fusion Protein (LayV-F) in Pre-Fusion Conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29029
TitleLangya Virus Fusion Protein (LayV-F) in Pre-Fusion Conformation
Map dataFinal 3D refinement
Sample
  • Complex: Langya Virus Fusion Protein Ectodomain Prefusion Conformation
    • Protein or peptide: Fusion Protein
KeywordsGlycoprotein / Fusion / Paramyxovirus / Henipavirus / Viral Protein
Biological speciesLangya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.64 Å
AuthorsMay AJ / Pothula KR / Janowska K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Virol / Year: 2023
Title: Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation.
Authors: Aaron J May / Karunakar Reddy Pothula / Katarzyna Janowska / Priyamvada Acharya /
Abstract: Langya virus (LayV) is a paramyxovirus in the genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following ...Langya virus (LayV) is a paramyxovirus in the genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following animal exposure in eastern China. Paramyxoviruses present two glycoproteins on their surface, known as attachment and fusion proteins, that mediate entry into cells and constitute the primary antigenic targets for immune response. Here, we determine cryo-electron microscopy (cryo-EM) structures of the uncleaved LayV fusion protein (F) ectodomain in pre- and postfusion conformations. The LayV-F protein exhibits pre- and postfusion architectures that, despite being highly conserved across paramyxoviruses, show differences in their surface properties, in particular at the apex of the prefusion trimer, that may contribute to antigenic variability. While dramatic conformational changes were visualized between the pre- and postfusion forms of the LayV-F protein, several domains remained invariant, held together by highly conserved disulfides. The LayV-F fusion peptide (FP) is buried within a highly conserved, hydrophobic interprotomer pocket in the prefusion state and is notably less flexible than the rest of the protein, highlighting its "spring-loaded" state and suggesting that the mechanism of pre-to-post transition must involve perturbations to the pocket and release of the fusion peptide. Together, these results offer a structural basis for how the Langya virus fusion protein compares to its Henipavirus relatives and propose a mechanism for the initial step of pre- to postfusion conversion that may apply more broadly to paramyxoviruses. The genus is quickly expanding into new animal hosts and geographic locations. This study compares the structure and antigenicity of the Langya virus fusion protein to other henipaviruses, which have important vaccine and therapeutic development implications. Furthermore, the study proposes a new mechanism to explain the early steps of the fusion initiation process that can be more broadly applied to the family.
History
DepositionDec 6, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29029.png

Downloads & links

-
Map

FileDownload / File: emd_29029.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal 3D refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.8782657 - 2.6222289
Average (Standard dev.)0.008948961 (±0.09842681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened map for model building

Fileemd_29029_additional_1.map
AnnotationSharpened map for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_29029_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_29029_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Langya Virus Fusion Protein Ectodomain Prefusion Conformation

EntireName: Langya Virus Fusion Protein Ectodomain Prefusion Conformation
Components
  • Complex: Langya Virus Fusion Protein Ectodomain Prefusion Conformation
    • Protein or peptide: Fusion Protein

-
Supramolecule #1: Langya Virus Fusion Protein Ectodomain Prefusion Conformation

SupramoleculeName: Langya Virus Fusion Protein Ectodomain Prefusion Conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 180 KDa

-
Macromolecule #1: Fusion Protein

MacromoleculeName: Fusion Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 59.02577 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLHYDSLSKV GIIKGLTYNY KIKGSPSTKL MVVKLIPNID GVRNCTQKQF DEYKNLVKNV LEPVKLALNA MLDNVKSGNN KYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI RGEINNNIIP V INQLSCDT ...String:
SLHYDSLSKV GIIKGLTYNY KIKGSPSTKL MVVKLIPNID GVRNCTQKQF DEYKNLVKNV LEPVKLALNA MLDNVKSGNN KYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI RGEINNNIIP V INQLSCDT IGLSVGIKLT QYYSEILTAF GPALQNPVNT RITIQAISSV FNRNFDELLK IMGYTSGDLY EILHSGLIRG NI IDVDVEA GYIALEIEFP NLTLVPNAVV QELMPISYNV DGDEWVTLVP RFVLTRTTLL SNIDTSRCTV TESSVICDND YAL PMSYEL IGCLQGDTSK CAREKVVSSY VPRFALSDGL VYANCLNTIC RCMDTDTPIS QSLGTTVSLL DNKKCLVYQV GDIL ISVGS YLGEGEYSAD NVELGPPVVI DKIDIGNQLA GINQTLQNAE DYIEKSEEFL KGINPSIGSG YIPEAPRDGQ AYVRK DGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6179 / Average electron dose: 56.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 13042103
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 195778
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-8fej:
Langya Virus Fusion Protein (LayV-F) in Pre-Fusion Conformation

+
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