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- EMDB-39238: The early intermediate structure of baculovirus fusion protein GP64 -

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Basic information

Entry
Database: EMDB / ID: EMD-39238
TitleThe early intermediate structure of baculovirus fusion protein GP64
Map data
Sample
  • Complex: GP64
    • Protein or peptide: Major envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


modulation by virus of host process / membrane fusion involved in viral entry into host cell / viral budding from plasma membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Baculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein family
Similarity search - Domain/homology
Major envelope glycoprotein
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsDu D / Guo J / Li S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971133 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural transition of GP64 triggered by a pH-sensitive multi-histidine switch.
Authors: Jinliang Guo / Shangrong Li / Lisha Bai / Huimin Zhao / Wenyu Shang / Zhaojun Zhong / Tuerxunjiang Maimaiti / Xueyan Gao / Ning Ji / Yanjie Chao / Zhaofei Li / Dijun Du /
Abstract: The fusion of viruses with cellular membranes is a critical step in the life cycle of enveloped viruses. This process is facilitated by viral fusion proteins, many of which are conformationally pH- ...The fusion of viruses with cellular membranes is a critical step in the life cycle of enveloped viruses. This process is facilitated by viral fusion proteins, many of which are conformationally pH-sensitive. The specifics of how changes in pH initiate this fusion have remained largely elusive. This study presents the cryo-electron microscopy (cryo-EM) structures of a prototype class III fusion protein, GP64, in its prefusion and early intermediate states, revealing the structural intermediates accompanying the membrane fusion process. The structures identify the involvement of a pH-sensitive switch, comprising H23, H245, and H304, in sensing the low pH that triggers the initial step of membrane fusion. The pH sensing role of this switch is corroborated by assays of cell-cell syncytium formation and dual dye-labeling. The findings demonstrate that coordination between multiple histidine residues acts as a pH sensor and activator. The involvement of a multi-histidine switch in viral fusion is applicable to fusogens of human-infecting thogotoviruses and other viruses, which could lead to strategies for developing anti-viral therapies and vaccines.
History
DepositionFeb 26, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39238.png

Downloads & links

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Map

FileDownload / File: emd_39238.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.11332385 - 0.4214149
Average (Standard dev.)0.0007568747 (±0.0101990495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39238_msk_1.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 : GP64

EntireName: GP64
Components
  • Complex: GP64
    • Protein or peptide: Major envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GP64

SupramoleculeName: GP64 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Autographa californica nucleopolyhedrovirus

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Macromolecule #1: Major envelope glycoprotein

MacromoleculeName: Major envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica nucleopolyhedrovirus
Molecular weightTheoretical: 53.338871 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HCNAQMKTGP YKIKNLDITP PKETLQKDVE ITIVETDYNE NVIIGYKGYY QAYAYNGGSL DPNTRVEETM KTLNVGKEDL LMWSIRQQC EVGEELIDRW GSDSDDCFRD NEGRGQWVKG KELVKRQNNN HFAHHTCNKS WRCGISTSKM YSRLECQDDT D ECQVYILD ...String:
HCNAQMKTGP YKIKNLDITP PKETLQKDVE ITIVETDYNE NVIIGYKGYY QAYAYNGGSL DPNTRVEETM KTLNVGKEDL LMWSIRQQC EVGEELIDRW GSDSDDCFRD NEGRGQWVKG KELVKRQNNN HFAHHTCNKS WRCGISTSKM YSRLECQDDT D ECQVYILD AEGNPINVTV DTVLHRDGVS MILKQKSTFT TRQIKAACLL IKDDKNNPES VTREHCLIDN DIYDLSKNTW NC KFNRCIK RKVEHRVKKR PPTWRHNVRA KYTEGDTATK GDLMHIQEEL MYENDLLKMN IELMHAHINK LNNMLHDLIV SVA KVDERL IGNLMNNSVS STFLSDDTFL LMPCTNPPAH TSNCYNNSIY KEGRWVANTD SSQCIDFSNY KELAIDDDVE FWIP TIGNT TYHDSWKDAS GWSFIAQQKS NLITTMENTK FGGVGTSLSD ITSMAEGELA AKLTSFMFGH

UniProtKB: Major envelope glycoprotein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.02 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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