9TCM | pdb_00009tcm

1.79 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under natural isotope abundance

PDB DOI: https://doi.org/10.2210/pdb9TCM/pdb
EM Map EMD-55792: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-21 Released: 2026-05-20
Deposition Author(s): Hakke, S.S., Noteborn, W.E.M., Knoops, K., Heeren, R.M.A.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9TCM

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

Literature

Isotope Decluttering Reduces Spectral Complexity While Maintaining Protein Structure

Hakke, S.S., Noteborn, W.E.M., Cabukusta, B., Gao, Y., Knoops, K., Lopez Iglesias, C., Kilgour, D.P.A., Clarke, D.J., Mathew, A., Heeren, R.M.A.

To be published.

Macromolecule Content

Total Structure Weight: 491.13 kDa
Atom Count: 34,281
Modeled Residue Count: 4,008
Deposited Residue Count: 4,344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin BfrB	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U [auth V], V [auth W], W [auth X], X [auth Y]	181	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: bfrB EC: 1.16.3.1
UniProt
Find proteins for P9WNE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNE5 Go to UniProtKB: P9WNE5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WNE5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Noteborn, W.E.M.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	15575

Revision History (Full details and data files)

Version 1.0: 2026-05-20
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.