9QFA | pdb_00009qfa

Structure of the GH13 and MucBP domains of Ruminococcus bromii Amy12

PDB DOI: https://doi.org/10.2210/pdb9QFA/pdb
EM Map EMD-53103: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Ruminococcus bromii L2-63
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-11 Released: 2025-10-22
Deposition Author(s): Wimmer, B.H., Medalia, O.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Spatial and expression-driven regulation of the Ruminococcus bromii amylosome in resistant starch degradation

Wimmer, B.H., Morais, S., Amit, I., Tovar-Herrera, O., Tatli, M., Trautwein-Schult, A., Toedtli, P., Simoni, S., Lisibach, M., Levin, L., Koropatkin, N., Becher, D., Bayer, E.A., Medalia, O., Mizrahi, I.

To be published.

Macromolecule Content

Total Structure Weight: 114.6 kDa
Atom Count: 5,871
Modeled Residue Count: 760
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ruminococcus bromii Amy12	A	1,040	Ruminococcus bromii L2-63	Mutation(s): 0 Gene Names: CBL15610.1 EC: 3.2.1.41
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	10000885

Revision History (Full details and data files)

Version 1.0: 2025-10-22
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.