[English] 日本語
Yorodumi
- EMDB-41636: Ghanaian virus fusion glycoprotein (GhV F) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41636
TitleGhanaian virus fusion glycoprotein (GhV F)
Map data
Sample
  • Complex: Prefusion Ghanian henipavirus F fused to the I53-50A trimer via an intervening 16 GS linker
    • Protein or peptide: Fusion glycoprotein F0,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGhV F / Glycoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Inhibitor / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Function / homology
Function and homology information


lyase activity / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
KDPG/KHG aldolase / KDPG and KHG aldolase / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fusion glycoprotein F0 / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesHenipavirus ghanaense / Thermotoga maritima MSB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPark YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure and design of Langya virus glycoprotein antigens.
Authors: Zhaoqian Wang / Matthew McCallum / Lianying Yan / Cecily A Gibson / William Sharkey / Young-Jun Park / Ha V Dang / Moushimi Amaya / Ashley Person / Christopher C Broder / David Veesler /
Abstract: Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which ...Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
History
DepositionAug 17, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41636.png

Downloads & links

-
Map

FileDownload / File: emd_41636.map.gz / Format: CCP4 / Size: 67 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 260 pix.
= 260. Å		1 Å/pix.
x 260 pix.
= 260. Å		1 Å/pix.
x 260 pix.
= 260. 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: 0.9
Minimum - Maximum-4.2997975 - 5.6787806
Average (Standard dev.)0.002704572 (±0.15169315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_41636_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41636_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41636_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Prefusion Ghanian henipavirus F fused to the I53-50A trimer via a...

EntireName: Prefusion Ghanian henipavirus F fused to the I53-50A trimer via an intervening 16 GS linker
Components
  • Complex: Prefusion Ghanian henipavirus F fused to the I53-50A trimer via an intervening 16 GS linker
    • Protein or peptide: Fusion glycoprotein F0,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Prefusion Ghanian henipavirus F fused to the I53-50A trimer via a...

SupramoleculeName: Prefusion Ghanian henipavirus F fused to the I53-50A trimer via an intervening 16 GS linker
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Henipavirus ghanaense

-
Macromolecule #1: Fusion glycoprotein F0,2-dehydro-3-deoxyphosphogluconate aldolase...

MacromoleculeName: Fusion glycoprotein F0,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Molecular weightTheoretical: 96.991531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKKTDNPTI SKRGHNHSRG IKSRALLRET DNYSNGLIVE NLVRNCHHPS KNNLNYTKTQ KRDSTIPYRV EERKGHYPKI KHLIDKSYK HIKRGKRRNG HNGNIITIIL LLILILKTQM SEGAIHYETL SKIGLIKGIT REYKVKGTPS SKDIVIKLIP N VTGLNKCT ...String:
MKKKTDNPTI SKRGHNHSRG IKSRALLRET DNYSNGLIVE NLVRNCHHPS KNNLNYTKTQ KRDSTIPYRV EERKGHYPKI KHLIDKSYK HIKRGKRRNG HNGNIITIIL LLILILKTQM SEGAIHYETL SKIGLIKGIT REYKVKGTPS SKDIVIKLIP N VTGLNKCT NISMENYKEQ LDKILIPINN IIELYANSTK SAPGNARFAG VIIAGVALGV AAAAQITAGI ALHEARQNAE RI NLLKDSI SATNNAVAEL QEATGGIVNV ITGMQDYINT NLVPQIDKLQ CSQIKTALDI SLSQYYSEIL TVFGPNLQNP VTT SMSIQA ISQSFGGNID LLLNLLGYTA NDLLDLLESK SITGQITYIN LEHYFMVIRV YYPIMTTISN AYVQELIKIS FNVD GSEWV SLVPSYILIR NSYLSNIDIS ECLITKNSVI CRHDFAMPMS YTLKECLTGD TEKCPREAVV TSYVPRFAIS GGVIY ANCL STTCQCYQTG KVIAQDGSQT LMMIDNQTCS IVRIEEILIS TGKYLGSQEY NTMHVSVGNP VFTDKLDITS QISNIN QSI EQSKFYLDKS KAILDKINLN LIGMKQIEDK IEEILSKIYH IENEIARIKK LIGEAPGGIE GRGGSGSGGS GGSGSEK AA KAEEAARKME ELFKKHKIVA VLRANSVEEA IEKAVAVFAG GVHLIEITFT VPDADTVIKA LSVLKEKGAI IGAGTVTS V EQARKAVESG AEFIVSPHLD EEISQFAKEK GVFYMPGVMT PTELVKAMKL GHTILKLFPG EVVGPQFVKA MKGPFPNVK FVPTGGVNLD NVAEWFKAGV LAVGVGSALV KGTPDEVREK AKAFVEKIRG ATEGGSGGSH HHHHHGSGGG SGLNDIFEAQ KIEWHE

UniProtKB: Fusion glycoprotein F0, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60207
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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