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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 / positive regulation of intracellular protein transport / anaphase-promoting complex-dependent catabolic process / gamma-tubulin complex / 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 / guanyl-nucleotide exchange factor activity / secretory granule / 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: To Be Published
Title: BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions
Authors: de Araujo, M.E.G. / Amann, S.J. / Stasyk, T. / Schleiffer, A. / Rauch, E. / Fluemann, P. / Singer, I. / Kremser, L. / Dostal, V. / Laopanupong, T. / Obojes, N. / Wallnoefer, M.H. / Gradl, F. ...Authors: de Araujo, M.E.G. / Amann, S.J. / Stasyk, T. / Schleiffer, A. / Rauch, E. / Fluemann, P. / Singer, I. / Kremser, L. / Dostal, V. / Laopanupong, T. / Obojes, N. / Wallnoefer, M.H. / Gradl, F.S. / Kurzbauer, R. / Krebiehl, C. / Kofler, S. / Grishkovskaya, I. / Vogel, G.F. / Hess, M.W. / Sarg, B. / Clausen, T. / Haselbach, D. / Huber, L.A.
History
DepositionDec 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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