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- EMDB-10279: CryoEM structure of SERINC from Drosophila melanogaster -

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Basic information

Entry
Database: EMDB / ID: EMD-10279
TitleCryoEM structure of SERINC from Drosophila melanogaster
Map datamain map - auto-sharpened by cryosparc
Sample
  • Complex: SERINC homo-hexamer
    • Protein or peptide: Membrane protein TMS1d
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CARDIOLIPIN
Function / homologySerine incorporator 2 / Serine incorporator/TMS membrane protein / Serine incorporator (Serinc) / phosphatidylserine metabolic process / sphingolipid metabolic process / membrane => GO:0016020 / membrane / Membrane protein TMS1d
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsPye VE / Nans A / Cherepanov P
Funding support United Kingdom, United States, 2 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001061 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150481 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: A bipartite structural organization defines the SERINC family of HIV-1 restriction factors.
Authors: Valerie E Pye / Annachiara Rosa / Cinzia Bertelli / Weston B Struwe / Sarah L Maslen / Robin Corey / Idlir Liko / Mark Hassall / Giada Mattiuzzo / Allison Ballandras-Colas / Andrea Nans / ...Authors: Valerie E Pye / Annachiara Rosa / Cinzia Bertelli / Weston B Struwe / Sarah L Maslen / Robin Corey / Idlir Liko / Mark Hassall / Giada Mattiuzzo / Allison Ballandras-Colas / Andrea Nans / Yasuhiro Takeuchi / Phillip J Stansfeld / J Mark Skehel / Carol V Robinson / Massimo Pizzato / Peter Cherepanov /
Abstract: The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of ...The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of human SERINC5 and its orthologue from Drosophila melanogaster at subnanometer and near-atomic resolution, respectively. The structures reveal a novel fold comprised of ten transmembrane helices organized into two subdomains and bisected by a long diagonal helix. A lipid binding groove and clusters of conserved residues highlight potential functional sites. A structure-based mutagenesis scan identified surface-exposed regions and the interface between the subdomains of SERINC5 as critical for HIV-1-restriction activity. The same regions are also important for viral sensitization to neutralizing antibodies, directly linking the antiviral activity of SERINC5 with remodeling of the HIV-1 envelope glycoprotein.
History
DepositionAug 30, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseJan 1, 2020-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6sp2
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10279.png

Downloads & links

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Map

FileDownload / File: emd_10279.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map - auto-sharpened by cryosparc
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-3.9277399 - 6.1650105
Average (Standard dev.)-0.00074485166 (±0.1364035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z386.400386.400386.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-3.9286.165-0.001

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Supplemental data

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Mask #1

Fileemd_10279_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: volume map without sharpening

Fileemd_10279_additional.map
Annotationvolume map without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_10279_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_10279_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SERINC homo-hexamer

EntireName: SERINC homo-hexamer
Components
  • Complex: SERINC homo-hexamer
    • Protein or peptide: Membrane protein TMS1d
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CARDIOLIPIN

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Supramolecule #1: SERINC homo-hexamer

SupramoleculeName: SERINC homo-hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: homo-hexamer of SERINC from Drosophila melanogaster recombinantly expressed and purified in detergent micelle; imaged as single particle.
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 328.05646 KDa

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Macromolecule #1: Membrane protein TMS1d

MacromoleculeName: Membrane protein TMS1d / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 54.721738 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGAALGICSA AQCAMCCGGT AASMCCSACP SCTNASSSRF MYAFILLVGT VLGAIALSPG LQDTLKKMPF CINSTSSYSS GALSAVSGG SLQVDCEYAL GYMAVYRVCF GMACFFALMS LIMLGVKSSR DPRSHIQNNF WPLKFLICFG AAIGAIFIPD G SFGPAMMW ...String:
MGAALGICSA AQCAMCCGGT AASMCCSACP SCTNASSSRF MYAFILLVGT VLGAIALSPG LQDTLKKMPF CINSTSSYSS GALSAVSGG SLQVDCEYAL GYMAVYRVCF GMACFFALMS LIMLGVKSSR DPRSHIQNNF WPLKFLICFG AAIGAIFIPD G SFGPAMMW VGLIGGLAFI LVQLVIIVDF AHSLAENWIE SAENSRGYYY ALAGVTLLCY ILSLTGITLL YIYFTTSTGC GI NKFFISI NLIFCLAISV ISILPAVQER LPHSGLLQSS LVTLYTVYLT WSAVANNPEK ECNPGMFGMM EGFGNATTTA APS THTTRV TFDTTNIIGL VVWLLCILYN CISSAVEVSK ISHDNSEKRV LTEALSDTEA GTDGSGKPST DTETEGVTYS WSMF HLVFV CASLYVMMTL TNWYKPHSEI ELFNGNEASM WVKIVSSWLG VFIYGWSLAA PIVLTNRDFS TGGSSGLEVL FQGPG SGGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

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Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 12 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #3: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 3 / Number of copies: 6 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #4: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 4 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.04 MNaClsodium chloride
0.01 MC8H18N2O4S-NaOHHEPES
0.5 mMC9H15O6PTCEP
0.5 mMHSCH2CH(OH)CH(OH)CH2SHDTT
0.0003 %C47H88O22LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: wait 60 seconds, blot for 3-4 seconds.
DetailsFreshly purified mono-dispersed sample

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2 / Details: 5,807 movies were collected
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1857080
Details: A sub-set of particles semi-automatically picked in EMAN2 Boxer were used to generate the starting 2D class averages, which, upon low-pass filtering to 20 A, served as templates for auto- ...Details: A sub-set of particles semi-automatically picked in EMAN2 Boxer were used to generate the starting 2D class averages, which, upon low-pass filtering to 20 A, served as templates for auto-picking of the entire dataset.
Startup modelType of model: NONE / Details: cryosparc ab initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Software - details: NuRefinement / Number images used: 159252
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2) / Software - details: ab initio
Final 3D classificationNumber classes: 9 / Avg.num./class: 59038 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 150.6 / Target criteria: Cross-correlation coefficient
Output model

PDB-6sp2:
CryoEM structure of SERINC from Drosophila melanogaster

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