[English] 日本語
Yorodumi
- EMDB-36045: The cryo-EM structure of PiB bound TMEM106B fibril. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36045
TitleThe cryo-EM structure of PiB bound TMEM106B fibril.
Map data
Sample
  • Tissue: The cryo-EM structure of PiB bound TMEM106B fibril.
    • Protein or peptide: Transmembrane protein 106B
KeywordsPROTEIN FIBRIL / amyloid
Function / homology
Function and homology information


lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane / ATPase binding / lysosome / endosome / lysosomal membrane / plasma membrane
Similarity search - Function
Transmembrane protein 106 / : / : / TM106 protein C-terminal domain / Transmembrane protein 106 N-terminal region
Similarity search - Domain/homology
Transmembrane protein 106B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao QY / Tao YQ / Yan F / Liu C / Li D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cryo-EM structure of PiB bound TMEM106B fibril.
Authors: Zhao QY / Tao YQ / Fan Y / Liu C / Li D
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36045.png

Downloads & links

-
Map

FileDownload / File: emd_36045.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00735
Minimum - Maximum-0.022529786 - 0.033544388
Average (Standard dev.)0.00015578124 (±0.0016727508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36045_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36045_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The cryo-EM structure of PiB bound TMEM106B fibril.

EntireName: The cryo-EM structure of PiB bound TMEM106B fibril.
Components
  • Tissue: The cryo-EM structure of PiB bound TMEM106B fibril.
    • Protein or peptide: Transmembrane protein 106B

-
Supramolecule #1: The cryo-EM structure of PiB bound TMEM106B fibril.

SupramoleculeName: The cryo-EM structure of PiB bound TMEM106B fibril. / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Transmembrane protein 106B

MacromoleculeName: Transmembrane protein 106B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.156318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ ...String:
MGKSLSHLPL HSSKEDAYDG VTSENMRNGL VNSEVHNEDG RNGDVSQFPY VEFTGRDSVT CPTCQGTGRI PRGQENQLVA LIPYSDQRL RPRRTKLYVM ASVFVCLLLS GLAVFFLFPR SIDVKYIGVK SAYVSYDVQK RTIYLNITNT LNITNNNYYS V EVENITAQ VQFSKTVIGK ARLNNITIIG PLDMKQIDYT VPTVIAEEMS YMYDFCTLIS IKVHNIVLMM QVTVTTTYFG HS EQISQER YQYVDCGRNT TYQLGQSEYL NVLQPQQ

UniProtKB: Transmembrane protein 106B

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.69 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84488
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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