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- PDB-7ru6: Cryo-EM structure of the HIV-1 restriction factor human SERINC3 -

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Basic information

Entry
Database: PDB / ID: 7ru6
TitleCryo-EM structure of the HIV-1 restriction factor human SERINC3
Components
  • Serine incorporator 3
  • SiA
KeywordsMEMBRANE PROTEIN / flippase / viral restriction / HIV-1
Function / homology
Function and homology information


Serine metabolism / L-serine transmembrane transporter activity / phospholipid scramblase activity / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / L-serine biosynthetic process / plasma membrane phospholipid scrambling / antiviral innate immune response / Golgi membrane / perinuclear region of cytoplasm / membrane / plasma membrane
Similarity search - Function
Serine incorporator/TMS membrane protein / Serine incorporator (Serinc)
Similarity search - Domain/homology
Serine incorporator 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPurdy, M.D. / Leonhardt, S.A. / Yeager, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P50AI150464-15 United States
Citation
Journal: Nat Commun / Year: 2023
Title: Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry.
Authors: Susan A Leonhardt / Michael D Purdy / Jonathan R Grover / Ziwei Yang / Sandra Poulos / William E McIntire / Elizabeth A Tatham / Satchal K Erramilli / Kamil Nosol / Kin Kui Lai / Shilei Ding ...Authors: Susan A Leonhardt / Michael D Purdy / Jonathan R Grover / Ziwei Yang / Sandra Poulos / William E McIntire / Elizabeth A Tatham / Satchal K Erramilli / Kamil Nosol / Kin Kui Lai / Shilei Ding / Maolin Lu / Pradeep D Uchil / Andrés Finzi / Alan Rein / Anthony A Kossiakoff / Walther Mothes / Mark Yeager /
Abstract: The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of ...The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionAug 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine incorporator 3
L: SiA


Theoretical massNumber of molelcules
Total (without water)80,6792
Polymers80,6792
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, electron microscopy, Negative Stain
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine incorporator 3 / Tumor differentially expressed protein 1 / hSERINC3


Mass: 55057.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERINC3, DIFF33, TDE1, SBBI99 / Plasmid: pFASTBAC1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q13530
#2: Antibody SiA


Mass: 25621.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: hSERINC3-SiA / Type: COMPLEX / Details: human WT SERINC3 with synthetic Fab SiA / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.055017 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFASTBAC1
Buffer solutionpH: 7.5
Details: Solutions were made fresh and filtered and degassed.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-{4-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.0045 percentdigitonin glyco-diosgeninC56H92O251
SpecimenConc.: 4 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: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: blot force 2 blot time 7

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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 / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8710
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.91/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Linux / Type: package
EM software
IDNameVersionCategory
1RELION3.1particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7Coot0.9.6model fitting
8ISOLDE1.2model fitting
9UCSF ChimeraX1.2model fitting
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
22PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 515000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 147 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient
Details: An initial hSERINC3 model was generated using AlphaFold v2.1 and the full database excluding PDB:6SP2. Low-confidence loops were removed from the model prior to fitting in the cryoEM map and ...Details: An initial hSERINC3 model was generated using AlphaFold v2.1 and the full database excluding PDB:6SP2. Low-confidence loops were removed from the model prior to fitting in the cryoEM map and side chains were retained.

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