+Open data
-Basic information
Entry | Database: PDB / ID: 7rug | ||||||
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Title | Human SERINC3-DeltaICL4 | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / flippase / viral restriction / HIV-1 | ||||||
Function / homology | Function and homology information Serine biosynthesis / L-serine transmembrane transporter activity / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / L-serine biosynthetic process / detection of virus / defense response to virus / Golgi membrane / innate immune response / perinuclear region of cytoplasm / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Purdy, M.D. / Leonhardt, S.A. / Yeager, M. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rug.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rug.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rug_validation.pdf.gz | 983.2 KB | Display | wwPDB validaton report |
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Full document | 7rug_full_validation.pdf.gz | 988.3 KB | Display | |
Data in XML | 7rug_validation.xml.gz | 23 KB | Display | |
Data in CIF | 7rug_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/7rug ftp://data.pdbj.org/pub/pdb/validation_reports/ru/7rug | HTTPS FTP |
-Related structure data
Related structure data | 24705MC 7ru6C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 52480.137 Da / Num. of mol.: 1 / Mutation: Delta 366-391 Source method: isolated from a genetically manipulated source Details: 26 residues from intracellular loop 4 deleted / Source: (gene. exp.) Homo sapiens (human) / Gene: SERINC3, DIFF33, TDE1, SBBI99 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q13530 |
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#2: Antibody | 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) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: hSERINC3-DeltaICL4-SiA / Type: COMPLEX / Details: human SERINC3-DeltaICL4 with synthetic Fab SiA / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.052440 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFASTBAC1 | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Solutions were made fresh and filtered and degassed. | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: blot force 2 blot time 7 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3438 |
-Processing
Software | Name: UCSF ChimeraX / Version: 0.91/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Linux / Type: package | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 433000 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 262 / 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. |