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- EMDB-52061: Sla2 C-terminal region (Residues 560-968) (REND and THATCH domains) -

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Basic information

Entry
Database: EMDB / ID: EMD-52061
TitleSla2 C-terminal region (Residues 560-968) (REND and THATCH domains)
Map data
Sample
  • Complex: ScSla2 residues 351-968
    • Protein or peptide: Protein SLA2
KeywordsActin binding / Endocytosis / membrane trafficking
Function / homology
Function and homology information


actin cortical patch assembly / clathrin light chain binding / incipient cellular bud site / negative regulation of Arp2/3 complex-mediated actin nucleation / cellular bud tip / actin cortical patch / clathrin coat assembly / clathrin adaptor activity / cellular bud neck / mating projection tip ...actin cortical patch assembly / clathrin light chain binding / incipient cellular bud site / negative regulation of Arp2/3 complex-mediated actin nucleation / cellular bud tip / actin cortical patch / clathrin coat assembly / clathrin adaptor activity / cellular bud neck / mating projection tip / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / clathrin-coated vesicle / cortical actin cytoskeleton / actin filament organization / endocytosis / actin filament binding / plasma membrane
Similarity search - Function
Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. ...Sla2 family / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / ENTH/VHS
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsDraper-Barr G / Gustavsson E / Landau M / Garcia-Alai MM
Funding support Germany, 1 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
CitationJournal: Structure / Year: 2025
Title: Sla2 is a core interaction hub for clathrin light chain and the Pan1/End3/Sla1 complex.
Authors: George Draper-Barr / Lucas A Defelipe / David Ruiz-Carrillo / Emil Gustavsson / Meytal Landau / Maria García-Alai /
Abstract: The interaction network of Sla2, a vital endocytic mid-coat adaptor protein, undergoes constant rearrangement. Sla2 serves as a scaffold linking the membrane to the actin cytoskeleton, with its role ...The interaction network of Sla2, a vital endocytic mid-coat adaptor protein, undergoes constant rearrangement. Sla2 serves as a scaffold linking the membrane to the actin cytoskeleton, with its role modulated by the clathrin light chain (CLC), which inhibits Sla2's function under certain conditions. We show that Sla2 has two independent binding sites for CLC: one previously described in homologs of fungi (Sla2) and metazoa (Hip1R), and a second found only in Fungi. We present the structural model of the Sla2 actin-binding domains in the context of regulatory structural domains by cryoelectron microscopy. We provide an interaction map of Sla2 and the regulatory proteins Sla1 and Pan1, predicted by AI modeling and confirmed by molecular biophysics techniques. Pan1 may compete with CLC for the conserved Sla2-binding site. These results enhance the mapping of crucial interactions at endocytic checkpoints and highlight the divergence between Metazoa and Fungi in this vital process.
History
DepositionNov 12, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52061.png

Downloads & links

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Map

FileDownload / File: emd_52061.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 170 pix.
= 231.2 Å		1.36 Å/pix.
x 170 pix.
= 231.2 Å		1.36 Å/pix.
x 170 pix.
= 231.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.19516215 - 0.5347696
Average (Standard dev.)0.0005274763 (±0.018205114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 231.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52061_msk_1.map
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Half map: #2

Fileemd_52061_half_map_1.map
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Half map: #1

Fileemd_52061_half_map_2.map
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Sample components

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Entire : ScSla2 residues 351-968

EntireName: ScSla2 residues 351-968
Components
  • Complex: ScSla2 residues 351-968
    • Protein or peptide: Protein SLA2

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Supramolecule #1: ScSla2 residues 351-968

SupramoleculeName: ScSla2 residues 351-968 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: ScSla2:351-968 forms a dimer through the coiled-coil and REND domain between residues 351-735.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Protein SLA2

MacromoleculeName: Protein SLA2 / type: protein_or_peptide / ID: 1
Details: Complete expression construct was residues 351-968 of ScSla2. Only residues 560-968 were able to be modelled into the electron density due to the inherent flexibility of the residues 351-559 ...Details: Complete expression construct was residues 351-968 of ScSla2. Only residues 560-968 were able to be modelled into the electron density due to the inherent flexibility of the residues 351-559 that form the coiled-coil.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.678672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ATAQMQPDFW ANQQAQFANE QNRLEQERVQ QLQQQQAQQE LFQQQLQKAQ QDMMNMQLQQ QNQHQNDLIA LTNQYEKDQA LLQQYDQRV QQLESEITTM DSTASKQLAN KDEQLTALQD QLDVWERKYE SLAKLYSQLR QEHLNLLPRF KKLQLKVNSA Q ESIQKKEQ ...String:
ATAQMQPDFW ANQQAQFANE QNRLEQERVQ QLQQQQAQQE LFQQQLQKAQ QDMMNMQLQQ QNQHQNDLIA LTNQYEKDQA LLQQYDQRV QQLESEITTM DSTASKQLAN KDEQLTALQD QLDVWERKYE SLAKLYSQLR QEHLNLLPRF KKLQLKVNSA Q ESIQKKEQ LEHKLKQKDL QMAELVKDRD RARLELERSI NNAEADSAAA TAAAETMTQD KMNPILDAIL ESGINTIQES VY NLDSPLS WSGPLTPPTF LLSLLESTSE NATEFATSFN NLIVDGLAHG DQTEVIHCVS DFSTSMATLV TNSKAYAVTT LPQ EQSDQI LTLVKRCARE AQYFFEDLMS ENLNQVGDEE KTDIVINANV DMQEKLQELS LAIEPLLNIQ SVKSNKETNP HSEL VATAD KIVKSSEHLR VDVPKPLLSL ALMIIDAVVA LVKAAIQCQN EIATTTSIPL NQFYLKNSRW TEGLISAAKA VAGAT NVLI TTASKLITSE DNENTSPEQF IVASKEVAAS TIQLVAASRV KTSIHSKAQD KLEHCSKDVT DACRSLGNHV MGMIED DHS TSQQQQPLDF TSEHTLKTAE MEQQVEILKL EQSLSNARKR LGEIRRHAYY NQDDD

UniProtKB: Protein SLA2

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.03 MHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
0.15 MNaClSodium Chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine

Details: 0.03 M HEPES pH 8 0.15 M NaCl 0.5 mM TCEP 0.1 um filtered buffer and degassed for one hour at room temperature
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse dimers of the ScSla2:351-968 construct

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
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

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: AF3 prediction of 2 moieties of ScSla2:560-968
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 249299
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8-f1


Chain - Residue range: 560-968 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: two chains of this model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: CC
Output model

PDB-9hdd:
Sla2 C-terminal region (Residues 560-968) (REND and THATCH domains)

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