9W3W | pdb_00009w3w

Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate

PDB DOI: https://doi.org/10.2210/pdb9W3W/pdb
EM Map EMD-65611: EMDB EMDataResource

Classification: IMMUNE SYSTEM/RNA
Organism(s): Actinomyces procaprae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-30 Released: 2026-03-04
Deposition Author(s): Lin, Z., Gao, H., Shi, R., Yang, M., Liu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate

Lin, Z., Gao, H., Shi, R., Yang, M., Liu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 348.29 kDa
Atom Count: 24,048
Modeled Residue Count: 3,152
Deposited Residue Count: 3,208
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm6	E [auth A], F [auth B], G [auth C], H [auth D]	797	Actinomyces procaprae	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PAPAPAPAP*A)-3')	A [auth 1], B [auth 2], C [auth 3], D [auth 4]	5	Actinomyces procaprae
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-03-04
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.