[English] 日本語
Yorodumi
- EMDB-20842: Endophilin B1 helical scaffold -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20842
TitleEndophilin B1 helical scaffold
Map dataHelical assembly of endophilin B1_N-BAR
Sample
  • Complex: Endophilin B1 helical assembly
    • Protein or peptide: Endophilin-B1
KeywordsMembrane binding / amphipathic helix / BAR protein / SH3 domain / membrane trafficking / cell death / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


protein localization to vacuolar membrane / positive regulation of membrane tubulation / autophagic cell death / positive regulation of autophagosome assembly / receptor catabolic process / membrane fission / membrane organization / positive regulation of protein targeting to mitochondrion / autophagosome membrane / regulation of macroautophagy ...protein localization to vacuolar membrane / positive regulation of membrane tubulation / autophagic cell death / positive regulation of autophagosome assembly / receptor catabolic process / membrane fission / membrane organization / positive regulation of protein targeting to mitochondrion / autophagosome membrane / regulation of macroautophagy / cellular response to glucose starvation / positive regulation of autophagy / cellular response to amino acid starvation / regulation of cytokinesis / positive regulation of protein-containing complex assembly / regulation of protein stability / autophagy / midbody / cytoplasmic vesicle / mitochondrial outer membrane / cadherin binding / Golgi membrane / lipid binding / apoptotic process / protein homodimerization activity / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...Endophilin-B1 / Endophilin-B1, BAR domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsBhatt VS / Sundborger-Lunna AC
CitationJournal: Structure / Year: 2021
Title: Amphipathic Motifs Regulate N-BAR Protein Endophilin B1 Auto-inhibition and Drive Membrane Remodeling.
Authors: Veer S Bhatt / Robert Ashley / Anna Sundborger-Lunna /
Abstract: Membrane remodeling is a common theme in a variety of cellular processes. Here, we investigated membrane remodeling N-BAR protein endophilin B1, a critical player in diverse intracellular trafficking ...Membrane remodeling is a common theme in a variety of cellular processes. Here, we investigated membrane remodeling N-BAR protein endophilin B1, a critical player in diverse intracellular trafficking events, including mitochondrial and Golgi fission, and apoptosis. We find that endophilin B1 assembles into helical scaffolds on membranes, and that both membrane binding and assembly are driven by interactions between N-terminal helix H0 and the lipid bilayer. Furthermore, we find that endophilin B1 membrane remodeling is auto-inhibited and identify direct SH3 domain-H0 interactions as the underlying mechanism. Our results indicate that lipid composition plays a role in dictating endophilin B1 activity. Taken together, this study provides insight into a poorly understood N-BAR protein family member and highlights molecular mechanisms that may be general for the regulation of membrane remodeling. Our work suggests that interplay between membrane lipids and membrane interacting proteins facilitates spatial and temporal coordination of membrane remodeling.
History
DepositionOct 17, 2019-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6upn
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6upn
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20842.png

Downloads & links

-
Map

FileDownload / File: emd_20842.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical assembly of endophilin B1_N-BAR
Voxel sizeX=Y=Z: 2.2942 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.03624512 - 0.062431928
Average (Standard dev.)0.0036417805 (±0.012786374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 490.9588 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.29420093457942.29420093457942.2942009345794
M x/y/z214214214
origin x/y/z0.0000.0000.000
length x/y/z490.959490.959490.959
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS214214214
D min/max/mean-0.0360.0620.004

-
Supplemental data

-
Sample components

-
Entire : Endophilin B1 helical assembly

EntireName: Endophilin B1 helical assembly
Components
  • Complex: Endophilin B1 helical assembly
    • Protein or peptide: Endophilin-B1

-
Supramolecule #1: Endophilin B1 helical assembly

SupramoleculeName: Endophilin B1 helical assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Endohilin B1 N-BAR domain
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Endophilin-B1

MacromoleculeName: Endophilin-B1 / type: protein_or_peptide / ID: 1 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.843246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNIMDFNVKK LAADAGTFLS RAVQFTEEKL GQAEKTELDA HLENLLSKAE CTKIWTEKIM KQTEVLLQPN PNARIEEFVY EKLDRKAPS RINNPELLGQ YMIDAGTEFG PGTAYGNALI KCGETQKRIG TADRELIQTS ALNFLTPLRN FIEGDYKTIA K ERKLLQNK ...String:
MNIMDFNVKK LAADAGTFLS RAVQFTEEKL GQAEKTELDA HLENLLSKAE CTKIWTEKIM KQTEVLLQPN PNARIEEFVY EKLDRKAPS RINNPELLGQ YMIDAGTEFG PGTAYGNALI KCGETQKRIG TADRELIQTS ALNFLTPLRN FIEGDYKTIA K ERKLLQNK RLDLDAAKTR LKKAKAAETR NSSEQELRIT QSEFDRQAEI TRLLLEGISS THAHHLRCLN DFVEAQMTYY AQ CYQYMLD LQKQLGSFPS NYLSNNNQTS VTPVPSVLPN AIGSSAMAST SGLVITSPSN LSDLKECSGS RKARVLYDYD AAN STELSL LADEVITVFS VVGMDSDWLM GERGNQKGKV PITYLELLN

UniProtKB: Endophilin-B1

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 8.1
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 17.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 59.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21197

+
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