9G2W

Endophilin B1 dimer bound to nanodisc edge

PDB DOI: https://doi.org/10.2210/pdb9G2W/pdb
EM Map EMD-50986: EMDB EMDataResource

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-11 Released: 2024-08-07
Deposition Author(s): Thorlacius, A., Sundborger-Lunna, A.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers

Thorlacius, A., Rulev, M., Sundberg, O., Sundborger-Lunna, A.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.08.07.606963

Macromolecule Content

Total Structure Weight: 81.69 kDa
Atom Count: 3,838
Modelled Residue Count: 478
Deposited Residue Count: 730
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endophilin-B1	A, B	365	Homo sapiens	Mutation(s): 0 Gene Names: SH3GLB1, KIAA0491, CGI-61
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y371 (Homo sapiens) Explore Q9Y371 Go to UniProtKB: Q9Y371
PHAROS: Q9Y371 GTEx: ENSG00000097033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y371
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Servalcat
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Sundborger-Lunna, A.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2021-05423

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release
Version 1.1: 2024-09-04
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.