9ZS4 | pdb_00009zs4

S. marcescens Cas10-Csm bound to target RNA

PDB DOI: https://doi.org/10.2210/pdb9ZS4/pdb
EM Map EMD-74688: EMDB EMDataResource
NAKB: 9ZS4

Classification: RNA BINDING PROTEIN
Organism(s): Serratia
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-12-22 Released: 2026-05-13
Deposition Author(s): Perdigao, C.C., Dokland, T., Dunkle, J.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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

Structural insights into target detection by the S. marcescens type III CRISPR complex and its deployment in SNP identification

Perdigao, C.C., Ajisafe, L.O., Sunny, A.T., Wu, S., Dokland, T., Dunkle, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 372.63 kDa
Atom Count: 23,910
Modeled Residue Count: 2,930
Deposited Residue Count: 3,176
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)	A	816	Serratia	Mutation(s): 0 Gene Names: cas10, CWC46_19900, Ser39006_019895
UniProt
Find proteins for A0A2I5TNR6 (Prodigiosinella confusarubida) Explore A0A2I5TNR6 Go to UniProtKB: A0A2I5TNR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I5TNR6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cms protein Csm2	D [auth B], E [auth C], F [auth D]	133	Serratia	Mutation(s): 0 Gene Names: csm2, CWC46_19905, Ser39006_019900
UniProt
Find proteins for A0A2I5TBC8 (Prodigiosinella confusarubida) Explore A0A2I5TBC8 Go to UniProtKB: A0A2I5TBC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I5TBC8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cms endoribonuclease Csm3	G [auth E], H [auth F], I [auth G], J [auth H]	248	Serratia	Mutation(s): 1 Gene Names: csm3, CWC46_19910, Ser39006_019905
UniProt
Find proteins for A0A2I5TNQ0 (Prodigiosinella confusarubida) Explore A0A2I5TNQ0 Go to UniProtKB: A0A2I5TNQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I5TNQ0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cms protein Csm4	K [auth I]	326	Serratia	Mutation(s): 0 Gene Names: CWC46_19915, Ser39006_019910
UniProt
Find proteins for A0A2I5TQV2 (Prodigiosinella confusarubida) Explore A0A2I5TQV2 Go to UniProtKB: A0A2I5TQV2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I5TQV2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cms protein Csm5	L [auth J]	559	Serratia	Mutation(s): 0 Gene Names: CWC46_19920, Ser39006_019915
UniProt
Find proteins for A0A2I5TBB3 (Prodigiosinella confusarubida) Explore A0A2I5TBB3 Go to UniProtKB: A0A2I5TBB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2I5TBB3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
crRNA	B [auth K]	42	Serratia
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
Target RNA	C [auth L]	42	Serratia
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-13

Deposition Author(s):

Perdigao, C.C.

Dokland, T.

Dunkle, J.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM142966
National Institutes of Health/Office of the Director	United States	S10OD024978