9E7J | pdb_00009e7j

Cu-bound tetrameric copper storage protein 1 with anti-rhodopsin 1D4 epitope

PDB DOI: https://doi.org/10.2210/pdb9E7J/pdb
EM Map EMD-47678: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Methylosinus trichosporium OB3b
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-01 Released: 2025-05-07
Deposition Author(s): Yao, Y., Oken, A.C., Farrens, D.L.
Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A novel "bio-tag" for cryo-EM studies based on the small, electron-dense protein Csp1

Yao, W., Oken, A.C., Farrens, D.L.

(2025) Biophys J

DOI: https://doi.org/10.1016/j.bpj.2025.03.018

Macromolecule Content

Total Structure Weight: 45.28 kDa
Atom Count: 3,112
Modelled Residue Count: 440
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Four-helix bundle copper-binding protein	A, B, C, D	110	Methylosinus trichosporium OB3b	Mutation(s): 0 Gene Names: CQW49_12740
UniProt
Find proteins for A0A2D2D105 (Methylosinus trichosporium OB3b) Explore A0A2D2D105 Go to UniProtKB: A0A2D2D105
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2D2D105
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	cryoSPARC	3.3

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01 EY029343

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

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.