7MI4 | pdb_00007mi4

Symmetrical PAM-PAM prespacer bound Cas4/Cas1/Cas2 complex

• PDB DOI: https://doi.org/10.2210/pdb7MI4/pdb
• NAKB: 7MI4
• EM Map EMD-23839: EMDB EMDataResource

• Classification: HYDROLASE/DNA
• Organism(s): Geobacter sulfurreducens PCA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-16 Released: 2021-11-17 
• Deposition Author(s): Hu, C.Y., Ke, A.K.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas.

Hu, C., Almendros, C., Nam, K.H., Costa, A.R., Vink, J.N.A., Haagsma, A.C., Bagde, S.R., Brouns, S.J.J., Ke, A.

(2021) Nature 598: 515-520

• PubMed: 34588691 
• DOI: https://doi.org/10.1038/s41586-021-03951-z
• Primary Citation Related Structures: 
  7MI4, 7MI5, 7MI9, 7MIB, 7MID


• PubMed Abstract: 
  

  Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array ¹ . Spacer insertion is carried out by the Cas1-Cas2 integrase complex ^2-4 . A substantial fraction of CRISPR-Cas systems use a Fe-S cluster containing Cas4 nuclease to ensure that spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM) ^5,6 and inserted into the CRISPR array unidirectionally, so that the transcribed CRISPR RNA can guide target searching in a PAM-dependent manner. Here we provide a high-resolution mechanistic explanation for the Cas4-assisted PAM selection, spacer biogenesis and directional integration by type I-G CRISPR in Geobacter sulfurreducens, in which Cas4 is naturally fused with Cas1, forming Cas4/Cas1. During biogenesis, only DNA duplexes possessing a PAM-embedded 3'-overhang trigger Cas4/Cas1-Cas2 assembly. During this process, the PAM overhang is specifically recognized and sequestered, but is not cleaved by Cas4. This 'molecular constipation' prevents the PAM-side prespacer from participating in integration. Lacking such sequestration, the non-PAM overhang is trimmed by host nucleases and integrated to the leader-side CRISPR repeat. Half-integration subsequently triggers PAM cleavage and Cas4 dissociation, allowing spacer-side integration. Overall, the intricate molecular interaction between Cas4 and Cas1-Cas2 selects PAM-containing prespacers for integration and couples the timing of PAM processing with the stepwise integration to establish directionality.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
Kavli Institute of Nanoscience, Delft, The Netherlands.
Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.
Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands. [e-mail].
Kavli Institute of Nanoscience, Delft, The Netherlands. [e-mail].
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 295.46 kDa 
• Atom Count: 17,162 
• Modeled Residue Count: 2,048 
• Deposited Residue Count: 2,496 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated exonuclease Cas4/endonuclease Cas1 fusion	A, B, C, D	559	Geobacter sulfurreducens PCA	Mutation(s): 0  Gene Names: cas4-cas1, GSU0057 EC: 3.1 (PDB Primary Data), 3.1.12.1 (PDB Primary Data)
UniProt
Find proteins for Q74H36 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74H36  Go to UniProtKB:  Q74H36

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas2	E, F	95	Geobacter sulfurreducens PCA	Mutation(s): 0  Gene Names: cas2, GSU0058 EC: 3.1
UniProt
Find proteins for Q74H35 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74H35  Go to UniProtKB:  Q74H35

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	G, H	35	Geobacter sulfurreducens PCA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	I [auth A], L [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MN	J [auth A], K [auth B], M [auth C], N [auth C], O [auth D], P [auth E], Q [auth F], R [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Hu, C.Y., Ke, A.K.

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.2: 2025-06-04
  Changes: Data collection