[English] 日本語
Yorodumi
- PDB-6upn: Endophilin B1 helical scaffold -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6upn
TitleEndophilin B1 helical scaffold
ComponentsEndophilin-B1
KeywordsCYTOSOLIC PROTEIN / Membrane binding / amphipathic helix / BAR protein / SH3 domain / membrane trafficking / cell death
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 / apoptotic process / lipid binding / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10 Å
AuthorsBhatt, V.S. / Sundborger-Lunna, A.C.
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-20842
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20842
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endophilin-B1
B: Endophilin-B1
C: Endophilin-B1
D: Endophilin-B1
E: Endophilin-B1
F: Endophilin-B1
G: Endophilin-B1
H: Endophilin-B1
I: Endophilin-B1
J: Endophilin-B1
K: Endophilin-B1
L: Endophilin-B1
M: Endophilin-B1
N: Endophilin-B1
O: Endophilin-B1
P: Endophilin-B1
Q: Endophilin-B1
R: Endophilin-B1
S: Endophilin-B1
T: Endophilin-B1
V: Endophilin-B1
W: Endophilin-B1
X: Endophilin-B1
Y: Endophilin-B1
a: Endophilin-B1
b: Endophilin-B1
c: Endophilin-B1
d: Endophilin-B1
e: Endophilin-B1
f: Endophilin-B1
g: Endophilin-B1
h: Endophilin-B1
i: Endophilin-B1
j: Endophilin-B1
k: Endophilin-B1
l: Endophilin-B1
m: Endophilin-B1
n: Endophilin-B1
o: Endophilin-B1
p: Endophilin-B1
q: Endophilin-B1
r: Endophilin-B1
s: Endophilin-B1
t: Endophilin-B1
v: Endophilin-B1
w: Endophilin-B1
x: Endophilin-B1
y: Endophilin-B1


Theoretical massNumber of molelcules
Total (without water)1,960,47648
Polymers1,960,47648
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Endophilin-B1 / Bax-interacting factor 1 / Bif-1 / SH3 domain-containing GRB2-like protein B1


Mass: 40843.246 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3GLB1, KIAA0491, CGI-61 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y371

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Endophilin B1 helical assembly / Type: COMPLEX / Details: Endohilin B1 N-BAR domain / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21DE3
Buffer solutionpH: 8.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 30 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 59.1 ° / Axial rise/subunit: 17.8 Å / Axial symmetry: C1
3D reconstructionResolution: 10 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21197 / Symmetry type: HELICAL

+
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