[English] 日本語
Yorodumi
- PDB-7a4a: Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) ... -

+
Open data


ID or keywords:

Loading...

-
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 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)
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11630
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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
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
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

+
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://pdbjlvh1.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