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- EMDB-72474: Sro7 bound to His-Exo84 (1-326) on a Nickel-NTA lipid monolayer -

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Basic information

Entry
Database: EMDB / ID: EMD-72474
TitleSro7 bound to His-Exo84 (1-326) on a Nickel-NTA lipid monolayer
Map dataB-factor sharpened map
Sample
  • Complex: Yeast Sro7 complexed with Exo84 (amino acids 1-326)
    • Protein or peptide: Lethal(2) giant larvae protein homolog SRO7
  • Ligand: SODIUM ION
KeywordsExocytosis / membrane trafficking / vesicle tethering
Function / homology
Function and homology information


myosin II binding / Golgi to plasma membrane transport / mating projection tip / syntaxin binding / small GTPase-mediated signal transduction / establishment of cell polarity / exocytosis / GTPase activator activity / SNARE binding / small GTPase binding ...myosin II binding / Golgi to plasma membrane transport / mating projection tip / syntaxin binding / small GTPase-mediated signal transduction / establishment of cell polarity / exocytosis / GTPase activator activity / SNARE binding / small GTPase binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Lethal giant larvae (Lgl)-like, C-terminal domain / Lethal giant larvae(Lgl) like, C-terminal / Trp-Asp (WD) repeats signature. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Lethal(2) giant larvae protein homolog SRO7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBaker RW / Strauss JD / McGinty RK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM150960 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM054712 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016086 United States
CitationJournal: J Struct Biol / Year: 2025
Title: Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM.
Authors: Aleksandra Skrajna / Clara Lenger / Emily Robinson / Kevin Cannon / Reta Sarsam / Richard G Ouellette / Alberta M Abotsi / Patrick Brennwald / Robert K McGinty / Joshua D Strauss / Richard W Baker /
Abstract: Grid preparation is a rate-limiting step in determining high-resolution structures by single particle cryo-EM. Particle interaction with the air-water interface often leads to denaturation, ...Grid preparation is a rate-limiting step in determining high-resolution structures by single particle cryo-EM. Particle interaction with the air-water interface often leads to denaturation, aggregation, or a preferred orientation within the ice. Some samples yield insufficient quantities of particles when using traditional grid making techniques and require the use of solid supports that concentrate samples onto the grid. Recent advances in grid-preparation show that affinity grids are promising tools to selectively concentrate proteins while simultaneously protecting samples from the air-water interface. One such technique utilizes lipid monolayers containing a lipid species with an affinity handle. Some of the first affinity grids used a holey carbon layer coated with nickel nitrilotriacetic acid (Ni-NTA) lipid, which allowed for the binding of proteins bearing the commonly used poly-histidine affinity tag. These studies however used complicated protocols and were conducted before the "resolution revolution" of cryo-EM. Here, we provide a straightforward preparation method and systematic analysis of Ni-NTA lipid monolayers as a tool for high-resolution single particle cryo-EM. We found the lipid affinity grids concentrate particles away from the AWI in thin ice (∼30 nm). We determined three structures ranging from 2.4 to 3.0 Å resolution, showing this method is amenable to high-resolution. Furthermore, we determined a 3.1 Å structure of a sub-100 kDa protein without symmetry, demonstrating the utility for a range of biological macromolecules. Lipid monolayers are therefore an easily extendable tool for most systems and help alleviate common problems such as low yield, disruption by the air-water interface, and thicker ice.
History
DepositionSep 2, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72474.png

Downloads & links

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Map

FileDownload / File: emd_72474.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.6222601 - 2.528555
Average (Standard dev.)-0.00013688944 (±0.037509795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72474_msk_1.map
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Additional map: Map for coloring by local resolution

Fileemd_72474_additional_1.map
AnnotationMap for coloring by local resolution
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Additional map: Map filtered by local resolution

Fileemd_72474_additional_2.map
AnnotationMap filtered by local resolution
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Additional map: unsharpened full map

Fileemd_72474_additional_3.map
Annotationunsharpened full map
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Additional map: deepEMhancer sharpened map

Fileemd_72474_additional_4.map
AnnotationdeepEMhancer sharpened map
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Half map: half map 1

Fileemd_72474_half_map_1.map
Annotationhalf map 1
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Half map: half map 2

Fileemd_72474_half_map_2.map
Annotationhalf map 2
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Sample components

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Entire : Yeast Sro7 complexed with Exo84 (amino acids 1-326)

EntireName: Yeast Sro7 complexed with Exo84 (amino acids 1-326)
Components
  • Complex: Yeast Sro7 complexed with Exo84 (amino acids 1-326)
    • Protein or peptide: Lethal(2) giant larvae protein homolog SRO7
  • Ligand: SODIUM ION

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Supramolecule #1: Yeast Sro7 complexed with Exo84 (amino acids 1-326)

SupramoleculeName: Yeast Sro7 complexed with Exo84 (amino acids 1-326) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Yeast Sro7 purified from yeast complexed with Exo84 (amino acids 1-326) purified recombinantly in E. coli.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Lethal(2) giant larvae protein homolog SRO7

MacromoleculeName: Lethal(2) giant larvae protein homolog SRO7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 114.639422 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFGSKRLKNV KEAFKSLKGQ NSETPIENSK ASFKSKNSKT STISKDAKSS SSLKIPISSN NKNKIFSLAE TNKYGMSSKP IAAAFDFTQ NLLAIATVTG EVHIYGQQQV EVVIKLEDRS AIKEMRFVKG IYLVVINAKD TVYVLSLYSQ KVLTTVFVPG K ITSIDTDA ...String:
MFGSKRLKNV KEAFKSLKGQ NSETPIENSK ASFKSKNSKT STISKDAKSS SSLKIPISSN NKNKIFSLAE TNKYGMSSKP IAAAFDFTQ NLLAIATVTG EVHIYGQQQV EVVIKLEDRS AIKEMRFVKG IYLVVINAKD TVYVLSLYSQ KVLTTVFVPG K ITSIDTDA SLDWMLIGLQ NGSMIVYDID RDQLSSFKLD NLQKSSFFPA ARLSPIVSIQ WNPRDIGTVL ISYEYVTLTY SL VENEIKQ SFIYELPPFA PGGDFSEKTN EKRTPKVIQS LYHPNSLHII TIHEDNSLVF WDANSGHMIM ARTVFETEIN VPQ PDYIRD SSTNAAKISK VYWMCENNPE YTSLLISHKS ISRGDNQSLT MIDLGYTPRY SITSYEGMKN YYANPKQMKI FPLP TNVPI VNILPIPRQS PYFAGCHNPG LILLILGNGE IETMLYPSGI FTDKASLFPQ NLSWLRPLAT TSMAASVPNK LWLGA LSAA QNKDYLLKGG VRTKRQKLPA EYGTAFITGH SNGSVRIYDA SHGDIQDNAS FEVNLSRTLN KAKELAVDKI SFAAET LEL AVSIETGDVV LFKYEVNQFY SVENRPESGD LEMNFRRFSL NNTNGVLVDV RDRAPTGVRQ GFMPSTAVHA NKGKTSA IN NSNIGFVGIA YAAGSLMLID RRGPAIIYME NIREISGAQS ACVTCIEFVI MEYGDDGYSS ILMVCGTDMG EVITYKIL P ASGGKFDVQL MDITNVTSKG PIHKIDAFSK ETKSSCLATI PKMQNLSKGL CIPGIVLITG FDDIRLITLG KSKSTHKGF KYPLAATGLS YISTVEKNND RKNLTVIITL EINGHLRVFT IPDFKEQMSE HIPFPIAAKY ITESSVLRNG DIAIRVSEFQ ASLFSTVKE QDTLAPVSDT LYINGIRIPY RPQVNSLQWA RGTVYCTPAQ LNELLGGVNR PASKYKESII AEGSFSERSS D DNNANHPE HQYTKPTRKG RNSSYGVLRN VSRAVETRWD AVEDRFNDYA TAMGETMNEA VEQTGKDVMK GALGF

UniProtKB: Lethal(2) giant larvae protein homolog SRO7

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS TALOS
DetailsBeam tilt compensation enabled and calibrated using SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

DetailsCounting mode
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: NU Refinement in cryoSPARC / Number images used: 524737
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2oaj


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9y48:
Sro7 bound to His-Exo84 (1-326) on a Nickel-NTA lipid monolayer

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