[English] 日本語
Yorodumi
- EMDB-62312: The cryoEM map of the hetero-octameric BLOC-one-related complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62312
TitleThe cryoEM map of the hetero-octameric BLOC-one-related complex
Map data
Sample
  • Complex: Octamer of BORCS1-8
    • Protein or peptide: BLOC-1 Related Complex subunit 1 (BORCS1)
    • Protein or peptide: BLOC-1 Related Complex subunit 2 (BORCS2)
    • Protein or peptide: BLOC-1 Related Complex subunit 3 (BORCS3)
    • Protein or peptide: BLOC-1 Related Complex subunit 4 (BORCS4)
    • Protein or peptide: BLOC-1 Related Complex subunit 5 (BORCS5)
    • Protein or peptide: BLOC-1 Related Complex subunit 6 (BORCS6)
    • Protein or peptide: BLOC-1 Related Complex subunit 7 (BORCS7)
    • Protein or peptide: BLOC-1 Related Complex subunit 8 (BORCS8)
Keywordslyososme binding / LIPID BINDING PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsGe X / Feng W
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Structure / Year: 2025
Title: The structure and assembly of the hetero-octameric BLOC-one-related complex.
Authors: Xuan Ge / Jinqi Ren / Kewei Gu / Weibin Gong / Kang Shen / Wei Feng /
Abstract: BORC (BLOC-one-related complex) is a hetero-octameric complex, consisting of eight coiled-coil proteins (BORCS1-8). BORC controls lysosomal and synaptic vesicle transport and positioning by ...BORC (BLOC-one-related complex) is a hetero-octameric complex, consisting of eight coiled-coil proteins (BORCS1-8). BORC controls lysosomal and synaptic vesicle transport and positioning by recruiting ARL8. The structural mechanisms underlying BORC assembly and ARL8 activation remain unclear. Here, we reconstitute and construct the structural model of this hetero-octameric complex. We find that BORC adopts an extended, rod-like structure made of coiled coils. Two hemicomplexes, each containing four subunits, are joined end-to-end to form the holocomplex. Within each hemicomplex, BORCS1/4/6/8 or BORCS2/3/5/7 assembles into similar helical bundles. We further study how BORC is built and discover a hierarchical assembly process in which BORCS1/2/3/5 forms the core scaffold and recruits other subunits. Mutations in the inter-hemicomplex interfaces result in two hemicomplexes. The association of ARL8 may require the proper assembly of BORC and is primarily mediated by BORCS5. These results provide guidance for further understanding of the biology of BORC.
History
DepositionNov 8, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62312.png

Downloads & links

-
Map

FileDownload / File: emd_62312.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 480 pix.
= 384. Å		0.8 Å/pix.
x 480 pix.
= 384. Å		0.8 Å/pix.
x 480 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.219
Minimum - Maximum-1.503585 - 1.4278548
Average (Standard dev.)0.0005136476 (±0.030021686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_62312_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62312_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62312_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Octamer of BORCS1-8

EntireName: Octamer of BORCS1-8
Components
  • Complex: Octamer of BORCS1-8
    • Protein or peptide: BLOC-1 Related Complex subunit 1 (BORCS1)
    • Protein or peptide: BLOC-1 Related Complex subunit 2 (BORCS2)
    • Protein or peptide: BLOC-1 Related Complex subunit 3 (BORCS3)
    • Protein or peptide: BLOC-1 Related Complex subunit 4 (BORCS4)
    • Protein or peptide: BLOC-1 Related Complex subunit 5 (BORCS5)
    • Protein or peptide: BLOC-1 Related Complex subunit 6 (BORCS6)
    • Protein or peptide: BLOC-1 Related Complex subunit 7 (BORCS7)
    • Protein or peptide: BLOC-1 Related Complex subunit 8 (BORCS8)

-
Supramolecule #1: Octamer of BORCS1-8

SupramoleculeName: Octamer of BORCS1-8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 130 KDa

-
Macromolecule #1: BLOC-1 Related Complex subunit 1 (BORCS1)

MacromoleculeName: BLOC-1 Related Complex subunit 1 (BORCS1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MLKEHSKKQH LRREVQEKLK NEAIVAAQTL STAVVDHLNA KVAQAYGNQK RLDVEAKRFE NNSAALAKQT EQWLFITEGL NYALKEIGDV ENWSKTIEND MKIITETLRR AYEAKNPPLP PNQANPASH

-
Macromolecule #2: BLOC-1 Related Complex subunit 2 (BORCS2)

MacromoleculeName: BLOC-1 Related Complex subunit 2 (BORCS2) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MAEINERAST SSPPVPSTPA PVPHIRQLAD NMTDKVGQFF QHQLEGSIEE YKLLETMNNT TAQRYVDMKV VAEKVAGKLD NLNQKYENLR PYLSQIDAMD ESTRRLEEAT AVLENYVTQL ESKLTNIQQQ SQ

-
Macromolecule #3: BLOC-1 Related Complex subunit 3 (BORCS3)

MacromoleculeName: BLOC-1 Related Complex subunit 3 (BORCS3) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MSSTAGGEVS INSGDLLLGT LSTSITKLEQ QIRATQLSQK KLNSDCETMA EYLRDLSEYK QPVDLLPYVG KLNDSTIRVN NTHQKLDDLL ERLTKLQRQI ARETYKKKNS IKEQEPPVQP EN

-
Macromolecule #4: BLOC-1 Related Complex subunit 4 (BORCS4)

MacromoleculeName: BLOC-1 Related Complex subunit 4 (BORCS4) / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MAEKNHQQQE RLPGNPFFPS RSNAGSSFDM PETPHLIDSL TSQIDEFTIQ SIIDTQRQSL KRFEKTNEML MNCAQLGDRR IEKAKRDSVG HKETILQMKT DLEFIFKKIR MFKTVLSSKY PEVYAEVSAE LTPKRSEEDE

-
Macromolecule #5: BLOC-1 Related Complex subunit 5 (BORCS5)

MacromoleculeName: BLOC-1 Related Complex subunit 5 (BORCS5) / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MGNEQSSSTA GTSSNPQNQQ SSFSFLTRAS TKRSKGIITV KDGNIPQEKL EDDEIYKRFT EIPRFLPVIP AVIGKRDPQT NQGASYTHQK ISSRPFFRLA TRLQEHFAVN AKAVAADQAK IPATCKSVEA KMIRLIEETR AHKEQHDGFM AALSGLNQLH DDICSIQIIL ...String:
MGNEQSSSTA GTSSNPQNQQ SSFSFLTRAS TKRSKGIITV KDGNIPQEKL EDDEIYKRFT EIPRFLPVIP AVIGKRDPQT NQGASYTHQK ISSRPFFRLA TRLQEHFAVN AKAVAADQAK IPATCKSVEA KMIRLIEETR AHKEQHDGFM AALSGLNQLH DDICSIQIIL EDIVPMVETL NEILTPDERL PPLNLGSVLD RSPVPSSDSS LQSTPRHNQN IGHIDQIEPI EEIRVVDLPK

-
Macromolecule #6: BLOC-1 Related Complex subunit 6 (BORCS6)

MacromoleculeName: BLOC-1 Related Complex subunit 6 (BORCS6) / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MSTSTESPDT PTTSQPLLSN KQTSFVVDDL EERIRESARI SSPKRAAAAG LPDPKILVDL ETHTKEIVNN MDTMLRDMRG SLHGMSDLTL ESLQCYNSGV EKACDEADAN VKSTYAMLAK VEEVNQSMGN VQKLAGQIKE MRRLVELFET LFHGSLK

-
Macromolecule #7: BLOC-1 Related Complex subunit 7 (BORCS7)

MacromoleculeName: BLOC-1 Related Complex subunit 7 (BORCS7) / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MSISLESKTK LPQKILEIIT DGSALLSIPM SSSQASETLL TSAKQFSHVE QVIDNTDKLL REIEQMVDGV TKNAEDMEKG LDIVCDVQEC LQKVERQNYY SAVPKSFSAD SFSSSVAGER PNPPNN

-
Macromolecule #8: BLOC-1 Related Complex subunit 8 (BORCS8)

MacromoleculeName: BLOC-1 Related Complex subunit 8 (BORCS8) / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MPDPSSTPNR TREIESRSRI ISERICESVR LLDNEPSLAL YRLQEHTVRS LPGLVNRRIM LTQQSATLSG AQFDLENTLS TTTSMQNATS AFDNCIELLR NCMFYKQQLD FDSTRKATSS AESSTVKGRS KSLHNVATRV HSTEASTSND A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Component - Concentration: 0.15 M / Component - Formula: NaCl / Component - Name: sodium chloride
GridModel: C-flat-1/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53274
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

+
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