9O59 | pdb_00009o59

ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle

PDB DOI: https://doi.org/10.2210/pdb9O59/pdb
EM Map EMD-70128: EMDB EMDataResource

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-09 Released: 2026-05-06
Deposition Author(s): Borst, A.J.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9O59

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

Literature

De novo design of metal-oxide templating proteins

Saragovi, A., Pyles, H., Borst, A.J., Baker, D.

To be published.

Macromolecule Content

Total Structure Weight: 99.71 kDa
Atom Count: 6,625
Modeled Residue Count: 852
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Z4-Cage Nanoparticle	A, B [auth D], C [auth G]	304	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
MODEL REFINEMENT	ISOLDE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.