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- EMDB-58431: Subtomogram average of SorCS2 dimer with additional docked beta-p... -

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Basic information

Entry
Database: EMDB / ID: EMD-58431
TitleSubtomogram average of SorCS2 dimer with additional docked beta-propeller
Map data
Sample
  • Complex: SorCS2 dimers on NTA(Ni)-functionalized liposomes
    • Protein or peptide: VPS10 domain-containing receptor SorCS2
KeywordsReceptor / Signaling / Sorting / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 11.5 Å
AuthorsBeugelink JW / Janssen BJC
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J Struct Biol X / Year: 2026
Title: Visualization of membrane-stabilized SorCS2 interactions.
Authors: J Wouter Beugelink / Bert J C Janssen /
Abstract: Members of the Vps10p receptor family regulate protein trafficking and cellular differentiation in the nervous system. Previous structural studies of the dimeric Vps10p family member SorCS2 have ...Members of the Vps10p receptor family regulate protein trafficking and cellular differentiation in the nervous system. Previous structural studies of the dimeric Vps10p family member SorCS2 have focused on isolated ectodomains, revealing substantial structural plasticity but overlooking the influence of the membrane association on receptor organization. Here we establish two complementary tools for reconstituting the SorCS2 ectodomain on proteoliposomes in its native orientation: non-covalent coupling via a C-terminal His-tag and nickel affinity, and covalent attachment via strain-promoted alkyne-azide cycloaddition using a C-terminal azide. We visualize the SorCS2 membrane-associated protein organization using electron cryo-tomography and obtain a nanometer resolution subtomogram average of the His-tag coupled SorCS2 ectodomain dimer. Four distinct, previously unreported, SorCS2 dimer-of-dimer arrangements are observed. The two most prominent interactions form through "head-to-side" docking of a Vps10p domain to the Vps10p and PKD core of another dimer, and "head-to-head" symmetric interactions between the Vps10p and SoMP domains of two dimers. Two less frequent assemblies comprise "side-by-side" interactions between the beta-propeller and 10CC domains and symmetrical "face-to-face" beta-propeller top face interactions. Together these interactions organize SorCS2 into two distinct helical arrangements and small receptor clusters on liposome surfaces. The promiscuity of membrane-stabilized SorCS2 interactions supports a more general mechanism in which the organization of receptor systems is influenced by membrane association. The tools presented here provide a versatile platform for visualizing ectodomain-mediated receptor assemblies in a membrane context.
History
DepositionJun 7, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58431.png

Downloads & links

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Map

FileDownload / File: emd_58431.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 240 pix.
= 825.6 Å		3.44 Å/pix.
x 240 pix.
= 825.6 Å		3.44 Å/pix.
x 240 pix.
= 825.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.008181751 - 0.021919124
Average (Standard dev.)0.000035329274 (±0.0017783712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 825.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_58431_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58431_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : SorCS2 dimers on NTA(Ni)-functionalized liposomes

EntireName: SorCS2 dimers on NTA(Ni)-functionalized liposomes
Components
  • Complex: SorCS2 dimers on NTA(Ni)-functionalized liposomes
    • Protein or peptide: VPS10 domain-containing receptor SorCS2

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Supramolecule #1: SorCS2 dimers on NTA(Ni)-functionalized liposomes

SupramoleculeName: SorCS2 dimers on NTA(Ni)-functionalized liposomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: VPS10 domain-containing receptor SorCS2

MacromoleculeName: VPS10 domain-containing receptor SorCS2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GARAVPVAGA ASASRAQVSL ISTSFVLKGD ATHNQAMVHW TGENSSVILI LTKYYHADMG KVLESSLWRS SDFGTTYTKL TLQPGVTTVI DNFYICPANK RKIILVSSSL GDREQSLFLS TDEGATFQKY PVPFLVETLL FHPKEEDKVL AYTKDSKLYV SSDLGKKWTL ...String:
GARAVPVAGA ASASRAQVSL ISTSFVLKGD ATHNQAMVHW TGENSSVILI LTKYYHADMG KVLESSLWRS SDFGTTYTKL TLQPGVTTVI DNFYICPANK RKIILVSSSL GDREQSLFLS TDEGATFQKY PVPFLVETLL FHPKEEDKVL AYTKDSKLYV SSDLGKKWTL LQERVTKDHV FWAVSGVDDD PNLVHVEAQD LSGGYRYYTC LIYNCSAQPH IAPFSGPIDR GSLTVQDEYI FLKATSTNRT KYYVSYRRSD FVLMKLPKYA LPKDLQIIST DEQQVFVAVQ EWNQVDTYNL YQSDLRGVRY SLVLENVRSS RQAEENVVID ILEVRGVKGV FLANQKVDGK VTTVITYNKG RDWDYLRPPS TDMNGKPTNC QPPDCYLHLH LRWADNPYVS GTVHTKDTAP GLIMGAGNLG SQLVEYKEEM YITSDCGHTW RQVFEEEHHV LYLDHGGVIA AIKDTSIPLK ILKFSVDEGH TWSTHNFTST SVFVDGLLSE PGDETLVMTV FGHISFRSDW ELVKVDFRPS FPRQCGEDDY SSWDLTDLQG DHCIMGQQRS YRKRKSTSWC VKGRSFTSAL TSRVCKCRDS DFLCDYGFER SSSSESTANK CSANFWFNPL SPPEDCVLGQ TYTSSLGYRK VVSNVCEGGV DLQQSPVQLQ CPLQAPRGLQ VSIRGEAVAV RPREDVLFVV RQEQGDVLTT KYQVDLGDGF KAMYVNLTLT GEPIRHHYES PGIYRVSVRA ENMAGHDEAV LFVQVNSPLQ ALYLEVVPVI GVNQEVNLTA VLLPLNPNLT VFYWWIGHSL QPLLSLDNSV TTKFTDAGDV RVTVQAACGN SVLQDSRLVR VLDQFQVVPL RFSRELDTFN PNTPEWREDV GLVVTRLLSK ETSIPEELLV TVVKPGLPTI ADLYVLLPLP RPTRKRSLTS DKRLAAVQQA LNSHRISFIL RGGLRILVEL RDTDTGPQRP GGSAAAHHHH HH

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Details: manual plunger.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.72 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 7398
ExtractionNumber tomograms: 58 / Number images used: 29400 / Software - Name: RELION (ver. 5.0)
CTF correctionSoftware - Name: CTFPHASEFLIP / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)

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Atomic model buiding 1

Initial modelPDB ID:

6ffy


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

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