9L7C | pdb_00009l7c

Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 1)

PDB DOI: https://doi.org/10.2210/pdb9L7C/pdb
EM Map EMD-62872: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Archaeoglobus fulgidus DSM 4304, Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-26 Released: 2025-12-31
Deposition Author(s): Ouchi, R., Numata, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A new in vitro reconstitution system of type III-B CRISPR-Cas effector for functional and structural studies

Ouchi, R., Numata, T.

To be published.

Macromolecule Content

Total Structure Weight: 405.92 kDa
Atom Count: 25,745
Modeled Residue Count: 3,322
Deposited Residue Count: 3,479
Unique protein chains: 6
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III-B CRISPR module RAMP protein Cmr4	A [auth F], B [auth D], C [auth E]	369	Archaeoglobus fulgidus DSM 4304	Mutation(s): 1 Gene Names: AF_1863
UniProt
Find proteins for O28416 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28416 Go to UniProtKB: O28416
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28416
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR system Cmr subunit Cmr5	D [auth H], E [auth G]	155	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: cmr5, AF_1862
UniProt
Find proteins for O28417 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28417 Go to UniProtKB: O28417
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28417
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III-B CRISPR module RAMP protein Cmr6	F [auth I]	343	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_1861
UniProt
Find proteins for O28418 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28418 Go to UniProtKB: O28418
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28418
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cmr1 C-terminal domain-containing protein	G [auth A]	329	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_1868
UniProt
Find proteins for O28411 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28411 Go to UniProtKB: O28411
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28411
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF domain-containing protein	H [auth B]	1,004	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_1867
UniProt
Find proteins for O28412 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28412 Go to UniProtKB: O28412
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28412
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III-B CRISPR module-associated protein Cmr3	I [auth C]	341	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_1866
UniProt
Find proteins for O28413 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28413 Go to UniProtKB: O28413
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28413
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Length	Organism	Image
Pf7.01 crRNA	J [auth V]	45	Pyrococcus furiosus DSM 3638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	L [auth B], M [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3.1
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Ouchi, R.

Numata, T.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16H04759
Japan Society for the Promotion of Science (JSPS)	Japan	16KK0166
Japan Society for the Promotion of Science (JSPS)	Japan	20H02916
Japan Society for the Promotion of Science (JSPS)	Japan	24H00505