7R2K | pdb_00007r2k

elongated Cascade complex from type I-A CRISPR-Cas system

PDB DOI: https://doi.org/10.2210/pdb7R2K/pdb
EM Map EMD-14245: EMDB EMDataResource
NAKB: 7R2K

Classification: ANTIVIRAL PROTEIN
Organism(s): Pyrococcus furiosus DSM 3638, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-04 Released: 2023-08-16
Deposition Author(s): Hu, C., Ni, D., Nam, K.H., Terns, M., Stahlberg, H., Ke, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural snapshots for an atypic type I CRISPR-Cas system

Ni, D., Hu, C., Nam, K.H., Terns, M., Stahlberg, H., Ke, A.

To be published.

Macromolecule Content

Total Structure Weight: 647.33 kDa
Atom Count: 43,931
Modeled Residue Count: 5,529
Deposited Residue Count: 5,672
Unique protein chains: 6
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated helicase Cas3	A	651	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: cas3, PFDSM3638_03195
UniProt
Find proteins for A0A5C0XNV5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore A0A5C0XNV5 Go to UniProtKB: A0A5C0XNV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C0XNV5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas11a	B [auth C] D [auth E] E [auth F] F [auth G] G [auth H] B [auth C], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J]	108	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF0643
UniProt
Find proteins for Q8U332 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U332 Go to UniProtKB: Q8U332
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U332
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas7a	J [auth K] K [auth L] L [auth M] M [auth N] N [auth O] J [auth K], K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], Q [auth R], S [auth T], U [auth V], V [auth W]	336	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF0642
UniProt
Find proteins for Q8U333 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U333 Go to UniProtKB: Q8U333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U333
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas3-HD	P [auth Q]	238	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: cas3, cas3'', PF0639 EC: 3.1
UniProt
Find proteins for Q8U336 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U336 Go to UniProtKB: Q8U336
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U336
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I-A CRISPR-associated protein Cas5	R [auth S]	256	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: cas5a, PFDSM3638_03200
UniProt
Find proteins for A0A5C0XNV9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore A0A5C0XNV9 Go to UniProtKB: A0A5C0XNV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C0XNV9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas8	X [auth Y]	341	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF0637
UniProt
Find proteins for Q8U338 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U338 Go to UniProtKB: Q8U338
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U338
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(PTPAPCPAPAPGPGPGP*A)-3')	C [auth D]	9	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 7
crRNA (57-MER)	T [auth U]	57	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
DNA (5'-D(PTPCPCPC)-3')	W [auth X]	4	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain Z [auth Q] SDF format, chain Y [auth Q] MOL2 format, chain Z [auth Q] MOL2 format, chain Y [auth Q] mmCIF format, chain Z [auth Q] mmCIF format, chain Y [auth Q]	Y [auth Q], Z [auth Q]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain Y [auth Q] Focus chain Z [auth Q] Interactions & Density Focus chain Y [auth Q] Focus chain Z [auth Q]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118117
Swiss National Science Foundation	Switzerland	(NCCR) TransCure
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118160