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- EMDB-11630: Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11630
TitleEnvelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm Ancylostoma ceylanicum
Map dataFinal EM map
Sample
  • Complex: Viral envelope glycoprotein
    • Protein or peptide: Integrase catalytic domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsclass II membrane fusion protein / retroviral envelope protein (Env) / lipid binding protein / disulfide bonding / VIRAL PROTEIN
Function / homology
Function and homology information


DNA integration / nucleic acid binding / membrane => GO:0016020
Similarity search - Function
Protein of unknown function DUF1759 / Retrotransposon, Pao / Peptidase aspartic, putative / Domain of unknown function DUF5641 / Protein of unknown function (DUF1759) / Pao retrotransposon peptidase / Putative peptidase (DUF1758) / Family of unknown function (DUF5641) / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain ...Protein of unknown function DUF1759 / Retrotransposon, Pao / Peptidase aspartic, putative / Domain of unknown function DUF5641 / Protein of unknown function (DUF1759) / Pao retrotransposon peptidase / Putative peptidase (DUF1758) / Family of unknown function (DUF5641) / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Integrase zinc-binding domain / Integrase zinc binding domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Integrase catalytic domain-containing protein
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsMata CP / Merchant M
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Wellcome Trust217191/Z/19/Z United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102869-01 United States
Citation
Journal: Sci Adv / Year: 2022
Title: A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus.
Authors: Monique Merchant / Carlos P Mata / Yangci Liu / Haoming Zhai / Anna V Protasio / Yorgo Modis /
Abstract: Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus ...Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus evolution. We identify Atlas virus-an intact retrovirus-like EVE in the human hookworm , with an envelope protein genetically related to G-G glycoproteins from the family Phenuiviridae. A cryo-EM structure of Atlas G reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas G has the structural hallmarks of an active fusogen. Atlas G trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas G has cell-cell fusion activity. With its preserved biological activities, Atlas G has the potential to acquire a cellular function. Our work reveals structural plasticity in reverse-transcribing RNA viruses.
#1: Journal: Biorxiv / Year: 2021
Title: A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus
Authors: Merchant M / Mata CP / Liu Y / Zhai H / Protasio AV / Modis Y
History
DepositionAug 19, 2020-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a4a
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11630.png

Downloads & links

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Map

FileDownload / File: emd_11630.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal EM map
Voxel sizeX=Y=Z: 1.047 Å
Density
Contour LevelBy AUTHOR: 0.0153 / Movie #1: 0.017
Minimum - Maximum-0.09405723 - 0.17276947
Average (Standard dev.)-0.000036032765 (±0.0043969885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 234.52802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z234.528234.528234.528
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-0.0940.173-0.000

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Supplemental data

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Mask #1

Fileemd_11630_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_11630_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_11630_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Viral envelope glycoprotein

EntireName: Viral envelope glycoprotein
Components
  • Complex: Viral envelope glycoprotein
    • Protein or peptide: Integrase catalytic domain-containing protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Viral envelope glycoprotein

SupramoleculeName: Viral envelope glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Envelope glycoprotein of endogenous retrovirus Y032 (Atlas virus) from Ancylostoma ceylanicum
Source (natural)Organism: Ancylostoma ceylanicum (invertebrata)
Molecular weightTheoretical: 143 KDa

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Macromolecule #1: Integrase catalytic domain-containing protein

MacromoleculeName: Integrase catalytic domain-containing protein / type: protein_or_peptide / ID: 1
Details: In chains A, B and C, residue Asn414 is covalently modified with an N-linked N-acetyl glucosamine ligand. Chains A, B and C each contain the following 15 disulfide bonds: Cys1-Cys41, Cys14- ...Details: In chains A, B and C, residue Asn414 is covalently modified with an N-linked N-acetyl glucosamine ligand. Chains A, B and C each contain the following 15 disulfide bonds: Cys1-Cys41, Cys14-Cys23, Cys66-Cys162, Cys87-Cys135, Cys93-Cys142, Cys98-Cys123, Cys127-Cys132, Cys129-Cys138, Cys246-Cys257, Cys264-Cys277, Cys266-Cys275, Cys337-Cys408, Cys347-Cys350, Cys360-Cys382, Cys373-Cys404.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ancylostoma ceylanicum (invertebrata)
Molecular weightTheoretical: 51.51909 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: CSEVISVTST EEVCTIQENK ETCTFNHATT ITLQPLQQQT CLTLNDPEKR PMGMLTVKPD GIKFRCNKKI EFFTRDHQIV SESVHRCHR AGSCHSDECH HVKDTDALPE FSSEANSRPG YTSCSSSCGC ITCDGCFFCE PSCLFHRLYA IPTTPTIYSI F YCPSWELE ...String:
CSEVISVTST EEVCTIQENK ETCTFNHATT ITLQPLQQQT CLTLNDPEKR PMGMLTVKPD GIKFRCNKKI EFFTRDHQIV SESVHRCHR AGSCHSDECH HVKDTDALPE FSSEANSRPG YTSCSSSCGC ITCDGCFFCE PSCLFHRLYA IPTTPTIYSI F YCPSWELE VDAEISLQRE DETTTSTIRL LPGRTSTWNN IRFSLIGTIV PQLPILSSAF VTNGRQTSIV KPAYAGQLQS NS VGQLQCP NLEAAKQFEC HFSRNLCTCT NALHKVSCTC YDGSVEDHME ALPLPQTSKN FLVFEKDRNI YAKTHVGSAL QLH IVAQDL KITTVKHTSH CQVEASDLSG CYSCTSGASL TLSCKSDNGE VLANMKCNEQ THVIRCTESG FINNILLMFD TSEV AADCT AACPGGIVNF TIKGLLAFVN ERIISQSYSA TDVERNIKGK PIPNPLLGLD STRTGHHHHH H

UniProtKB: Integrase catalytic domain-containing protein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 3 / 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

Concentration0.025 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMNH12C4O3ClTris/HCl
0.1 MNaClsodium chloride
5.0 %C3H8O3glycerol
0.5 mMC9H15O6PTCEP

Details: 20 mM Tris/HCl (NH12C4O3Cl) 0.1 M NaCl 'sodium chloride' 5 % glycerol (C3H8O3) 0.5 mM TCEP (C9H15O6P)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.2 K / Instrument: FEI VITROBOT MARK IV / Details: Grids were blotted for 4 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: None / Chromatic aberration corrector: None / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 3027 / Average exposure time: 8.0 sec. / Average electron dose: 46.18 e/Å2 / Details: Dose rate = 1.28 e- A^-2 per frame
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMovies were motion-corrected and dose-weighted with MOTIONCOR2.
Particle selectionNumber selected: 987570
Details: 2D references from initial datasets were used to auto-pick the micrographs. One round of reference-free 2D classification was performed to produce templates for better reference-dependent auto-picking.
Startup modelType of model: OTHER
Details: Micrographs from initial datasets allowed us to obtain a model at 19 A resolution from 3,790 particles. This model was filtered at 40 A resolution and used as the initial model for 3D classification.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 197145
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6egu


Chain - Chain ID: A / Chain - Residue range: 691-1136 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: A homology model was built from PDB:6EGU using the Swiss-Model server (swissmodel.expasy.org). The model was docked as a rigid body into the density with UCSF Chimera prior to refinement.
DetailsA homology model was built from PDB:6EGU using the Swiss-Model server (swissmodel.expasy.org). The model was docked as a rigid body into the density with UCSF Chimera prior to refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 82 / Target criteria: Cross-correlation coefficient
Output model

PDB-7a4a:
Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm Ancylostoma ceylanicum

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