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- EMDB-10277: Cryo-EM structure of human SERINC5 in LMNG micelles, bound to Fab. -

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Basic information

Entry
Database: EMDB / ID: EMD-10277
TitleCryo-EM structure of human SERINC5 in LMNG micelles, bound to Fab.
Map datasharpened EM map
Sample
  • Complex: complex of SERINC5 with FAB bound to ECL4 in LMNG micelles
    • Protein or peptide: SERINC5
    • Protein or peptide: FAB (antigen binding fragment from a monoclonal antibody)
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsRosa A / Pye VE / Nans A / Cherepanov P
Funding support United States, United Kingdom, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP50 AI150481 United States
The Francis Crick InstituteFC001061 United Kingdom
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) releaseSep 11, 2019-
Map releaseJan 1, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10277.png

Downloads & links

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Map

FileDownload / File: emd_10277.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 140 pix.
= 305.2 Å		2.18 Å/pix.
x 140 pix.
= 305.2 Å		2.18 Å/pix.
x 140 pix.
= 305.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.06572661 - 0.1380292
Average (Standard dev.)-0.00004616876 (±0.005605059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 305.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z305.200305.200305.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0660.138-0.000

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Supplemental data

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Additional map: unsharpened EM map

Fileemd_10277_additional.map
Annotationunsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened EM map

Fileemd_10277_additional_1.map
Annotationunsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map 2

Fileemd_10277_half_map_1.map
AnnotationEM half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map 1

Fileemd_10277_half_map_2.map
AnnotationEM half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of SERINC5 with FAB bound to ECL4 in LMNG micelles

EntireName: complex of SERINC5 with FAB bound to ECL4 in LMNG micelles
Components
  • Complex: complex of SERINC5 with FAB bound to ECL4 in LMNG micelles
    • Protein or peptide: SERINC5
    • Protein or peptide: FAB (antigen binding fragment from a monoclonal antibody)

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Supramolecule #1: complex of SERINC5 with FAB bound to ECL4 in LMNG micelles

SupramoleculeName: complex of SERINC5 with FAB bound to ECL4 in LMNG micelles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: SERINC5

MacromoleculeName: SERINC5 / type: protein_or_peptide / ID: 1
Details: Full-length, wild type human SERINC5 with C-terminal TwinStrep tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: msaqccagql acccgsagcs lccdccprir qslstrfmya lyfilvvvlc cimmsttvah kmkehipffe dmckgikagd tceklvgysa vyrvcfgmac fffifclltl kinnskscra hihngfwffk llllgamcsg affipdqdtf lnawryvgav ggflfigiql ...String:
msaqccagql acccgsagcs lccdccprir qslstrfmya lyfilvvvlc cimmsttvah kmkehipffe dmckgikagd tceklvgysa vyrvcfgmac fffifclltl kinnskscra hihngfwffk llllgamcsg affipdqdtf lnawryvgav ggflfigiql lllvefahkw nknwtagtas nklwyaslal vtlimysiat gglvlmavfy tqkdscmenk illgvngglc llislvaisp wvqnrqphsg llqsgviscy vtyltfsals skpaevvlde hgknvticvp dfgqdlyrde nlvtilgtsl ligcilyscl tsttrsssda lqgryaapel eiarccfcfs pggedteeqq pgkegprviy dekkgtvyiy syfhfvffla slyvmmtvtn wfnyesanie sffsgswsif wvkmascwic vllylctlva plccptrefs vgssglevlf qgpgsggsaw shpqfekggg sgggsggsaw shpqfek

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Macromolecule #2: FAB (antigen binding fragment from a monoclonal antibody)

MacromoleculeName: FAB (antigen binding fragment from a monoclonal antibody)
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
amino acid sequence unknown

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.04 MNaClsodium chloride
0.01 MHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
GridModel: C-flat-1.2/1.3 4C / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Details: No pre-treatment
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex was assembled using recombinant SERINC5 in LMNG/PS and FAB and was purified by size exclusion chromatograhy immediately prior to vitrification on holey carbon EM grids.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 7165 / Average electron dose: 33.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2502546
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: OTHER / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 270151
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 11 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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