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- PDB-7a4a: Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) ... -

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Basic information

Entry
Database: PDB / ID: 7a4a
TitleEnvelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm Ancylostoma ceylanicum
ComponentsIntegrase catalytic domain-containing protein
KeywordsVIRAL PROTEIN / class II membrane fusion protein / retroviral envelope protein (Env) / lipid binding protein / disulfide bonding
Function / homology
Function and homology information


DNA polymerase complex / DNA integration / nucleic acid binding / membrane
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) / Immunoglobulin-like - #3770 / Phlebovirus glycoprotein G2, fusion 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) / Immunoglobulin-like - #3770 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrase catalytic domain-containing protein
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsMata, C.P. / Merchant, M. / Modis, Y.
Funding support United Kingdom, United States, 3items
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, C.P. / Liu, Y. / Zhai, H. / Protasio, A.V. / Modis, Y.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 25, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list / em_admin / pdbx_database_related / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _em_3d_fitting_list.accession_code ..._citation.journal_id_ISSN / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Integrase catalytic domain-containing protein
B: Integrase catalytic domain-containing protein
C: Integrase catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2216
Polymers154,5573
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18760 Å2
ΔGint-63 kcal/mol
Surface area51100 Å2
MethodPISA

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Components

#1: Protein Integrase catalytic domain-containing protein


Mass: 51519.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Gene: Acey_s0020.g108, Y032_0020g108 / Plasmid: pMT/BiP/V5-His / Cell line (production host): d.mel-2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A016UZK2
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Viral envelope glycoprotein / Type: COMPLEX
Details: Envelope glycoprotein of endogenous retrovirus Y032 (Atlas virus) from Ancylostoma ceylanicum
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.143 MDa / Experimental value: YES
Source (natural)Organism: Ancylostoma ceylanicum (invertebrata)
Source (recombinant)Organism: Drosophila melanogaster (fruit fly) / Cell: d.mel-2 / Plasmid: pMT/BiP/V5-His
Buffer solutionpH: 8
Details: 20 mM Tris/HCl (NH12C4O3Cl) 0.1 M NaCl 'sodium chloride' 5 % glycerol (C3H8O3) 0.5 mM TCEP (C9H15O6P)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris/HClNH12C4O3Cl1
20.1 Msodium chlorideNaCl1
35 %glycerolC3H8O31
40.5 mMTCEPC9H15O6P1
SpecimenConc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.2 K / Details: Grids were blotted for 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 46.18 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3027 / Details: Dose rate = 1.28 e- A^-2 per frame
EM imaging opticsEnergyfilter name: GIF Quantum LS / Chromatic aberration corrector: None / Energyfilter slit width: 20 eV / Phase plate: OTHER / Spherical aberration corrector: None
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 36

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPU1.9.1image acquisition
4Gctf0.5CTF correction
7UCSF Chimera1.13.1model fitting
9PHENIX1.15rc3-3435model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
Image processingDetails: Movies were motion-corrected and dose-weighted with MOTIONCOR2.
CTF correctionDetails: Aligned, non-dose-weighted micrographs were then used to estimate the CTF.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles 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.
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197145 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 82 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
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.
Atomic model buildingPDB-ID: 6EGU

6egu


Pdb chain-ID: A / Accession code: 6EGU
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.
Pdb chain residue range: 691-1136 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00710362
ELECTRON MICROSCOPYf_angle_d0.67314073
ELECTRON MICROSCOPYf_dihedral_angle_d21.0863765
ELECTRON MICROSCOPYf_chiral_restr0.0431659
ELECTRON MICROSCOPYf_plane_restr0.0051821

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