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- EMDB-24705: Human SERINC3-DeltaICL4 -

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Basic information

Entry
Database: EMDB / ID: EMD-24705
TitleHuman SERINC3-DeltaICL4
Map datahSERINC3-Delta26 masked and sharpened cryo-EM map
Sample
  • Complex: hSERINC3-DeltaICL4-SiA
    • Protein or peptide: Serine incorporator 3
    • Protein or peptide: SiA
Keywordsflippase / viral restriction / HIV-1 / UNKNOWN FUNCTION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsPurdy MD / Leonhardt SA / Yeager M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P50AI150464-15 United States
CitationJournal: 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 17, 2021-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24705.png

Downloads & links

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Map

FileDownload / File: emd_24705.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhSERINC3-Delta26 masked and sharpened cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 200 pix.
= 201. Å		1.01 Å/pix.
x 200 pix.
= 201. Å		1.01 Å/pix.
x 200 pix.
= 201. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.0316351 - 0.06709909
Average (Standard dev.)0.00025391797 (±0.0021827829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 201.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24705_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hSERINC3-Delta26 RELION Refine3D half map

Fileemd_24705_half_map_1.map
AnnotationhSERINC3-Delta26 RELION Refine3D half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hSERINC3-Delta26 RELION Refine3D half map

Fileemd_24705_half_map_2.map
AnnotationhSERINC3-Delta26 RELION Refine3D half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hSERINC3-DeltaICL4-SiA

EntireName: hSERINC3-DeltaICL4-SiA
Components
  • Complex: hSERINC3-DeltaICL4-SiA
    • Protein or peptide: Serine incorporator 3
    • Protein or peptide: SiA

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Supramolecule #1: hSERINC3-DeltaICL4-SiA

SupramoleculeName: hSERINC3-DeltaICL4-SiA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: human SERINC3-DeltaICL4 with synthetic Fab SiA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.44 KDa

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Macromolecule #1: Serine incorporator 3

MacromoleculeName: Serine incorporator 3 / type: protein_or_peptide / ID: 1 / Details: 26 residues from intracellular loop 4 deleted / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.480137 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGAVLGVFSL ASWVPCLCSG ASCLLCSCCP NSKNSTVTRL IYAFILLLST VVSYIMQRKE METYLKKIPG FCEGGFKIHE ADINADKDC DVLVGYKAVY RISFAMAIFF FVFSLLMFKV KTSKDLRAAV HNGFWFFKIA ALIGIMVGSF YIPGGYFSSV W FVVGMIGA ...String:
MGAVLGVFSL ASWVPCLCSG ASCLLCSCCP NSKNSTVTRL IYAFILLLST VVSYIMQRKE METYLKKIPG FCEGGFKIHE ADINADKDC DVLVGYKAVY RISFAMAIFF FVFSLLMFKV KTSKDLRAAV HNGFWFFKIA ALIGIMVGSF YIPGGYFSSV W FVVGMIGA ALFILIQLVL LVDFAHSWNE SWVNRMEEGN PRLWYAALLS FTSAFYILSI ICVGLLYTYY TKPDGCTENK FF ISINLIL CVVASIISIH PKIQEHQPRS GLLQSSLITL YTMYLTWSAM SNEPDRSCNP NLMSFITRIT APTLAPGNST AVV PTPTPP SKSGSLLDSD NFIGLFVFVL CLLYSSIRTS TNSQVDKLTR AVDNEKEGVQ YSYSLFHLML CLASLYIMMT LTSW YSPDA KFQSMTSKWP AVWVKISSSW VCLLLYVWTL VAPLVLTSRD FSLEENLYFQ GGSWSHPQFE KAS

UniProtKB: Serine incorporator 3

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Macromolecule #2: SiA

MacromoleculeName: SiA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.621412 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSSSSIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARFYSRYSWY GYSYGWSRAF DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NFSSSSIHWV RQAPGKGLEW VASISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARFYSRYSWY GYSYGWSRAF DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT C

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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

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S2-{4-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMNaClsodium chloride
0.0045 percentC56H92O25digitonin glyco-diosgenin

Details: Solutions were made fresh and filtered and degassed.
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 2 blot time 7.

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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: 3438 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 433000
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 140000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsAn 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.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 262 / Target criteria: Correlation Coefficient
Output model

PDB-7rug:
Human SERINC3-DeltaICL4

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