[English] 日本語
Yorodumi
- EMDB-56129: Octameric C. elegans BORC, containing BORCS5, BORCS6, BORCS7, BOR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56129
TitleOctameric C. elegans BORC, containing BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and the shared BORC and BLoC-1 subunits, BLOC1S1, BLOC1S2 and Snapin
Map data
Sample
  • Complex: BORC
    • Protein or peptide: Biogenesis of lysosome-related organelles complex 1 subunit 1
    • Protein or peptide: Biogenesis of lysosome-related organelles complex 1 subunit 2
    • Protein or peptide: SNAPIN protein homolog
    • Protein or peptide: KxDL domain-containing protein
    • Protein or peptide: BLOC-1-related complex subunit 5
    • Protein or peptide: BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein
    • Protein or peptide: BLOC-1-related complex subunit 7
    • Protein or peptide: BLOC-1-related complex subunit 8 homolog
KeywordsBORC / BLOC-1 / lysosome / recycling endosome / EARP / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsAmann SJ / de Araujo MEG / Grishkovskaya I / Huber LA / Haselbach D
Funding support Austria, 1 items
OrganizationGrant numberCountry
Other private Austria
CitationJournal: To Be Published
Title: BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions
Authors: de Araujo MEG / Amann SJ / Stasyk T / Schleiffer A / Rauch E / Fluemann P / Singer I / Kremser L / Dostal V / Laopanupong T / Obojes N / Wallnoefer MH / Gradl FS / Kurzbauer R / Krebiehl C / ...Authors: de Araujo MEG / Amann SJ / Stasyk T / Schleiffer A / Rauch E / Fluemann P / Singer I / Kremser L / Dostal V / Laopanupong T / Obojes N / Wallnoefer MH / Gradl FS / Kurzbauer R / Krebiehl C / Kofler S / Grishkovskaya I / Vogel GF / Hess MW / Sarg B / Clausen T / Haselbach D / Huber LA
History
DepositionDec 19, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_56129.png

Downloads & links

-
Map

FileDownload / File: emd_56129.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 300 pix.
= 481.5 Å		1.61 Å/pix.
x 300 pix.
= 481.5 Å		1.61 Å/pix.
x 300 pix.
= 481.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.605 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.0026868954 - 2.1958704
Average (Standard dev.)0.00026451342 (±0.012546198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 481.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_56129_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_56129_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_56129_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_56129_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_56129_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BORC

EntireName: BORC
Components
  • Complex: BORC
    • Protein or peptide: Biogenesis of lysosome-related organelles complex 1 subunit 1
    • Protein or peptide: Biogenesis of lysosome-related organelles complex 1 subunit 2
    • Protein or peptide: SNAPIN protein homolog
    • Protein or peptide: KxDL domain-containing protein
    • Protein or peptide: BLOC-1-related complex subunit 5
    • Protein or peptide: BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein
    • Protein or peptide: BLOC-1-related complex subunit 7
    • Protein or peptide: BLOC-1-related complex subunit 8 homolog

-
Supramolecule #1: BORC

SupramoleculeName: BORC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

-
Macromolecule #1: Biogenesis of lysosome-related organelles complex 1 subunit 1

MacromoleculeName: Biogenesis of lysosome-related organelles complex 1 subunit 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 14.698619 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLKEHSKKQH LRREVQEKLK NEAIVAAQTL STAVVDHLNA KVAQAYGNQK RLDVEAKRFE NNSAALAKQT EQWLFITEGL NYALKEIGD VENWSKTIEN DMKIITETLR RAYEAKNPPL PPNQANPASH

UniProtKB: Biogenesis of lysosome-related organelles complex 1 subunit 1

-
Macromolecule #2: Biogenesis of lysosome-related organelles complex 1 subunit 2

MacromoleculeName: Biogenesis of lysosome-related organelles complex 1 subunit 2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 15.013739 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAEINERAST SSPPVPSTPA PVPHIRQLAD NMTDKVGQFF QHQLEGSIEE YKLLETMNNT TAQRYVDMKV VAEKVAGKLD NLNQKYENL RPYLSQIDAM DESTRRLEEA TAVLENYVTQ LESKLTNIQQ QSQ

UniProtKB: Biogenesis of lysosome-related organelles complex 1 subunit 2

-
Macromolecule #3: SNAPIN protein homolog

MacromoleculeName: SNAPIN protein homolog / type: protein_or_peptide / ID: 3
Details: MSSTAGGEVSINSGDLLLGTLSTSITKLEQQIRATQLSQKKLNSDCETMAEYLRDLSEYKQPVDLLPYVGKLNDSTIRVNNTHQKLDDLLERLTKLQRQIARETYKKKNSIKEQEPPVQPEN
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 13.837612 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSTAGGEVS INSGDLLLGT LSTSITKLEQ QIRATQLSQK KLNSDCETMA EYLRDLSEYK QPVDLLPYVG KLNDSTIRVN NTHQKLDDL LERLTKLQRQ IARETYKKKN SIKEQEPPVQ PEN

UniProtKB: SNAPIN protein homolog

-
Macromolecule #4: KxDL domain-containing protein

MacromoleculeName: KxDL domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis (invertebrata)
Molecular weightTheoretical: 16.295448 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAEKNHQQQE RLPGNPFFPS RSNAGSSFDM PETPHLIDSL TSQIDEFTIQ SIIDTQRQSL KRFEKTNEML MNCAQLGDRR IEKAKRDSV GHKETILQMK TDLEFIFKKI RMFKTVLSSK YPEVYAEVSA ELTPKRSEED E

UniProtKB: KxDL domain-containing protein

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

MacromoleculeName: BLOC-1-related complex subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 26.732188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANEQSSSTA GTSSNPQNQQ SSFSFLTRAS TKRSKGIITV KDGNIPQEKL EDDEIYKRFT EIPRFLPVIP AVIGKRDPQT NQGASYTHQ KISSRPFFRL ATRLQEHFAV NAKAVAADQA KIPATCKSVE AKMIRLIEET RAHKEQHDGF MAALSGLNQL H EDICSIQI ...String:
MANEQSSSTA GTSSNPQNQQ SSFSFLTRAS TKRSKGIITV KDGNIPQEKL EDDEIYKRFT EIPRFLPVIP AVIGKRDPQT NQGASYTHQ KISSRPFFRL ATRLQEHFAV NAKAVAADQA KIPATCKSVE AKMIRLIEET RAHKEQHDGF MAALSGLNQL H EDICSIQI ILEDIVPMVE TLNEILTPDE RLPPLNLGSV LDRSPVPSSD SSLQSTPRHN QNIGHIDQIE PIEEIRVVDL PK

UniProtKB: BLOC-1-related complex subunit 5

-
Macromolecule #6: BLOC-1-related complex subunit 6 C-terminal helix domain-containi...

MacromoleculeName: BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein
type: protein_or_peptide / ID: 6
Details: MSTSTESPDTPTTSQPLLSNKQTSFVVDDLEERIRESARISSPKRAAAAGLPDPKILVDLETHTKEIVNNMDTMLRDMRGSLHGMSDLTLESLQCYNSGVEKACDEADANVKSTYAMLAKVEEVNQSMGNVQKLAGQIKEMRRLVELFETLFHGSLKENLYFQ
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 18.177521 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTSTESPDT PTTSQPLLSN KQTSFVVDDL EERIRESARI SSPKRAAAAG LPDPKILVDL ETHTKEIVNN MDTMLRDMRG SLHGMSDLT LESLQCYNSG VEKACDEADA NVKSTYAMLA KVEEVNQSMG NVQKLAGQIK EMRRLVELFE TLFHGSLKEN L YFQ

UniProtKB: BLOC-1-related complex subunit 6 C-terminal helix domain-containing protein

-
Macromolecule #7: BLOC-1-related complex subunit 7

MacromoleculeName: BLOC-1-related complex subunit 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 13.864539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSISLESKTK LPQKILEIIT DGSALLSIPM SSSQASETLL TSAKQFSHVE QVIDNTDKLL REIEQMVDGV TKNAEDMEKG LDIVCDVQE CLQKVERQNY YSAVPKSFSA DSFSSSVAGE RPNPPNN

UniProtKB: BLOC-1-related complex subunit 7

-
Macromolecule #8: BLOC-1-related complex subunit 8 homolog

MacromoleculeName: BLOC-1-related complex subunit 8 homolog / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 16.878781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPDPSSTPNR TREIESRSRI ISERICESVR LLDNEPSLAL YRLQEHTVRS LPGLVNRRIM LTQQSATLSG AQFDLENTLS TTTSMQNAT SAFDNCIELL RNCMFYKQQL DFDSTRKATS SAESSTVKGR SKSLHNVATR VHSTEASTSN DA

UniProtKB: BLOC-1-related complex subunit 8 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaCl
0.5 mMTCEP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 201956
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9tqb:
Octameric C. elegans BORC, containing BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and the shared BORC and BLoC-1 subunits, BLOC1S1, BLOC1S2 and Snapin

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more