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- PDB-9tqb: Octameric C. elegans BORC, containing BORCS5, BORCS6, BORCS7, BOR... -

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Basic information

Entry
Database: PDB / ID: 9tqb
TitleOctameric C. elegans BORC, containing BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and the shared BORC and BLoC-1 subunits, BLOC1S1, BLOC1S2 and Snapin
Components
  • (BLOC-1-related complex subunit ...) x 4
  • (Biogenesis of lysosome-related organelles complex 1 subunit ...) x 2
  • KxDL domain-containing protein
  • SNAPIN protein homolog
KeywordsTRANSPORT PROTEIN / BORC / BLOC-1 / lysosome / recycling endosome / EARP
Function / homology
Function and homology information


BLOC complex / BORC complex / positive regulation of nematode pharyngeal pumping / positive regulation of gut granule assembly / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of anterograde synaptic vesicle transport / cytoplasmic side of lysosomal membrane / BLOC-1 complex / organelle transport along microtubule ...BLOC complex / BORC complex / positive regulation of nematode pharyngeal pumping / positive regulation of gut granule assembly / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of anterograde synaptic vesicle transport / cytoplasmic side of lysosomal membrane / BLOC-1 complex / organelle transport along microtubule / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / gamma-tubulin complex / positive regulation of intracellular protein transport / lysosome localization / positive regulation of multicellular organism growth / gamma-tubulin binding / locomotion / endosomal transport / lysosome organization / endosome to lysosome transport / synaptic vesicle transport / synaptic vesicle exocytosis / regulation of mitotic cell cycle / secretory granule / guanyl-nucleotide exchange factor activity / SNARE binding / intracellular protein transport / mitochondrial intermembrane space / synaptic vesicle / synaptic vesicle membrane / mitochondrial matrix / lysosomal membrane / cytosol
Similarity search - Function
Biogenesis of lysosome-related organelles complex 1 subunit 1 / Snapin / BLOC-1-related complex subunit 5 / Biogenesis of lysosome-related organelles complex-1, subunit 2 / BLOC-1-related complex subunit 6 / BLOC-1-related complex subunit 8 / Uncharacterised domain KxDL / Snapin/Pallidin/Snn1 / BLOC-1-related complex subunit 7 / KxDL motif-containing protein 1-like ...Biogenesis of lysosome-related organelles complex 1 subunit 1 / Snapin / BLOC-1-related complex subunit 5 / Biogenesis of lysosome-related organelles complex-1, subunit 2 / BLOC-1-related complex subunit 6 / BLOC-1-related complex subunit 8 / Uncharacterised domain KxDL / Snapin/Pallidin/Snn1 / BLOC-1-related complex subunit 7 / KxDL motif-containing protein 1-like / BLOC-1-related complex subunit 6, C-terminal helix / GCN5-like protein 1 (GCN5L1) / Biogenesis of lysosome-related organelles complex-1 subunit 2 / BLOC-1-related complex sub-unit 6 C-terminal helix / Tumour suppressor protein / BLOC-1-related complex sub-unit 8 / Uncharacterized conserved protein / Snapin/Pallidin / BLOC-1-related complex sub-unit 7
Similarity search - Domain/homology
KxDL domain-containing protein / BLOC-1-related complex subunit 5 / SNAPIN protein homolog / BLOC-1-related complex subunit 8 homolog / BLOC-1-related complex subunit 7 / Biogenesis of lysosome-related organelles complex 1 subunit 1 / Biogenesis of lysosome-related organelles complex 1 subunit 2 / BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Caenorhabditis (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsAmann, S.J. / de Araujo, M.E.G. / Grishkovskaya, I. / Huber, L.A. / Haselbach, D.
Funding support Austria, 1items
OrganizationGrant numberCountry
Other private Austria
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions.
Authors: Mariana E G de Araujo / Sascha J Amann / Taras Stasyk / Alexander Schleiffer / Eva Rauch / Paula Flümann / Isabel I Singer / Leopold Kremser / Vojtech Dostal / Thanida Laopanupong / ...Authors: Mariana E G de Araujo / Sascha J Amann / Taras Stasyk / Alexander Schleiffer / Eva Rauch / Paula Flümann / Isabel I Singer / Leopold Kremser / Vojtech Dostal / Thanida Laopanupong / Nikolaus Obojes / Moritz H Wallnöfer / Flora S Gradl / Robert Kurzbauer / Caroline Krebiehl / Samuel Kofler / Irina Grishkovskaya / Georg F Vogel / Michael W Hess / Bettina Sarg / Tim Clausen / David Haselbach / Lukas A Huber /
Abstract: BORC and BLOC-1 are multisubunit complexes that regulate endolysosomal trafficking. Although they are presumed to be distinct, their paralogous origins and shared subunits suggest the potential for ...BORC and BLOC-1 are multisubunit complexes that regulate endolysosomal trafficking. Although they are presumed to be distinct, their paralogous origins and shared subunits suggest the potential for higher-order assembly. Here, we reveal the conserved octameric architecture of BORC formed by two intertwined tetramers and present the structure of C. elegans BORC. Through cross-linking mass spectrometry of endogenous complexes, we validate this model for human BORC and demonstrate that the integrity of the complex, which is essential for lysosomal transport, relies on specific interfacial residues. We also clarify the disruptive nature of disease-causing mutations and propose that the formation and function of BORC are likely regulated by specific cues. These cues might include the phosphorylation of Snapin and a pH-sensitive histidine residue in BORCS5. Additionally, we present direct biochemical and structural evidence of BORC-BLOC-1 hybrid complexes. Finally, we link a specific hybrid complex to the regulation of transferrin receptor recycling via interaction with the EARP complex. Our work challenges the paradigm of BORC and BLOC-1 as separate entities, establishing a model of dynamic complex formation wherein modular assembly creates functional specialization to meet diverse cellular demands.
History
DepositionDec 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
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Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Biogenesis of lysosome-related organelles complex 1 subunit 1
H: Biogenesis of lysosome-related organelles complex 1 subunit 2
F: SNAPIN protein homolog
E: KxDL domain-containing protein
A: BLOC-1-related complex subunit 5
B: BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein
C: BLOC-1-related complex subunit 7
D: BLOC-1-related complex subunit 8 homolog


Theoretical massNumber of molelcules
Total (without water)135,4988
Polymers135,4988
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Biogenesis of lysosome-related organelles complex 1 subunit ... , 2 types, 2 molecules GH

#1: Protein Biogenesis of lysosome-related organelles complex 1 subunit 1 / BLOC-1 subunit 1


Mass: 14698.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: blos-1, T20G5.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q22616
#2: Protein Biogenesis of lysosome-related organelles complex 1 subunit 2 / BLOC-1 subunit 2


Mass: 15013.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: blos-2, Y73B6BL.30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95XD3

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Protein , 2 types, 2 molecules FE

#3: Protein SNAPIN protein homolog / Biogenesis of lysosome-related organelles complex 1 subunit 7 / BLOC-1 subunit 7


Mass: 13837.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MSSTAGGEVSINSGDLLLGTLSTSITKLEQQIRATQLSQKKLNSDCETMAEYLRDLSEYKQPVDLLPYVGKLNDSTIRVNNTHQKLDDLLERLTKLQRQIARETYKKKNSIKEQEPPVQPEN
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: snpn-1, C02B10.2 / Production host: Escherichia coli (E. coli) / References: UniProt: O44445
#4: Protein KxDL domain-containing protein


Mass: 16295.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis (invertebrata) / Gene: kxd-1, C13F10.2, CELE_C13F10.2 / Production host: Escherichia coli (E. coli) / References: UniProt: O01488

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BLOC-1-related complex subunit ... , 4 types, 4 molecules ABCD

#5: Protein BLOC-1-related complex subunit 5


Mass: 26732.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sam-4, CELE_F59E12.11, F59E12.11 / Production host: Escherichia coli (E. coli) / References: UniProt: O01902
#6: Protein BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein


Mass: 18177.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MSTSTESPDTPTTSQPLLSNKQTSFVVDDLEERIRESARISSPKRAAAAGLPDPKILVDLETHTKEIVNNMDTMLRDMRGSLHGMSDLTLESLQCYNSGVEKACDEADANVKSTYAMLAKVEEVNQSMGNVQKLAGQIKEMRRLVELFETLFHGSLKENLYFQ
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: blos-7, CELE_Y37E11B.3, Y37E11B.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TYN4
#7: Protein BLOC-1-related complex subunit 7


Mass: 13864.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: blos-8, CELE_R03A10.1, R03A10.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21655
#8: Protein BLOC-1-related complex subunit 8 homolog


Mass: 16878.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: blos-9, K11B4.2 / Production host: Escherichia coli (E. coli) / References: UniProt: O45685

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BORC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21DE3 / Plasmid: pET23
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2150 mMsodium chlorideNaCl1
30.5 mMTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201956 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 310.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325958
ELECTRON MICROSCOPYf_angle_d0.60258030
ELECTRON MICROSCOPYf_chiral_restr0.0368947
ELECTRON MICROSCOPYf_plane_restr0.00641044
ELECTRON MICROSCOPYf_dihedral_angle_d5.8931795

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